From owner-chemistry@ccl.net Tue May 2 03:10:00 2006 From: "Barbault Florent florent.barbault:-:paris7.jussieu.fr" To: CCL Subject: CCL: help needed Message-Id: <-31648-060501125605-3365-rd8ELvMq2lQkuN0FHuevVQ{}server.ccl.net> X-Original-From: "Barbault Florent" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Mon, 01 May 2006 17:45:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Barbault Florent" [florent.barbault[A]paris7.jussieu.fr] Hi, My answer will certainly not please you. I already had this problem of analysing large energetical data with molecular dynamics simulations. I think the best solution is to write a software in perl, c or fortran languages to find the minimum, the maximum and the rms. Your software will be very quick to find these parameters. The problem will be to write this program. For your first software you will need long times for doing it, but it will be very easy for the next. Sincerely yours Florent On Mon, 1 May 2006 08:20:34 -0400 "Richard L. Wood rwoodphd:msn.com" wrote: > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > Hi all, > > This question isn't a direct computational chemistry question, but >an indirect one. So please bear with me. > > I'm trying to analyze the output of a 1 nanosecond MD calculation >that I ran using the program NAMD. Since it's a text file, I could >use MS Excel to open it and sort the energies from lowest to highest >value, which is what I would like to do. However, MS Excel has a >limit of about 65000 lines of text (or rows) that a file can contain. > Mine has 2000000 lines of text, so that my file is too big. My >workaround is to open the file in MS Word, and cut it into pieces >that can be opened in MS Excel. Then I can find the minimum energy >fro each piece, save that value, and then when done, find the overall >minimum. Once I've done this, I can find the corresponding frame >number in the file that contained it, go to the trajectory and save >those coordinates. > > However, as you can imagine, this isn't a very efficient process. > My simulation takes about 2 and half hours or so to run, while this >analysis takes about two hours to do. I can therefore do about one >of these in a day, as I have another non-computational "job" that I >am doing. At some point, I will be running some smalled >calculations, which will take much less than two hours to run, and so >the analysis will take longer than the simulation! > > My question is this: does anyone know of a spreadsheat program >where I can a) import a text file of more than 65000 rows easily, b) >can sort a given column of that file, and c) works under Windows and >is free? I've tried Quattro Pro, and all the file comes out in a >single row! > > TIA, > Richard > > > > -= This is automatically added to each message by the mailing script >=- > To recover the email address of the author of the message, please >change> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >search)> > > From owner-chemistry@ccl.net Tue May 2 03:45:00 2006 From: "forli(_)unisi.it" To: CCL Subject: CCL: Converting coordinates Message-Id: <-31649-060501193206-17018-/OPCiZJpfbZAuHI1LWn7lQ[-]server.ccl.net> X-Original-From: forli]*[unisi.it Date: Mon, 01 May 2006 22:37:52 +0200 (MET-DST) Sent to CCL by: forli_+_unisi.it OpenBabel does it, and is released under GNU/public licence (free use). Hope it helps, Stefano >Sent to CCL by: "Juan Gil" [dagur99**hotmail.com] >I'm interested in conversion methods from internal to cartesian coordinates for academic use. Any information is welcome, thanks a lot.> > > --- *********************************** Stefano Forli Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 e-mail: forli]=[unisi.it *********************************** From owner-chemistry@ccl.net Tue May 2 05:29:00 2006 From: "mehdi.bounouar=-=ch.tum.de (Mehdi Bounouar)" To: CCL Subject: CCL: help needed Message-Id: <-31650-060502052543-7810-0AQh6FE/YKWOvV8XugobHA-x-server.ccl.net> X-Original-From: mehdi.bounouar]|[ch.tum.de (Mehdi Bounouar) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 2 May 2006 10:31:59 +0200 MIME-Version: 1.0 Sent to CCL by: mehdi.bounouar##ch.tum.de (Mehdi Bounouar) Hello, My 2cents, try a language like python, the learning curve is much less steeper than the others especially if you don't know much perl, c or fortran, besides it is very well supported for Windows and has larger community to which you can submit your problem. Something like this is a start, it sorts the nth column and skips lines that cannot be converted: import string import Numeric column = 0 file = open("filename.dat") data = [] line = file.readline() while line != '': try: map(float,string.split(line))[column] except: line = file.readline() data.append(map(float,string.split(line))[column]) line = file.readline() data.sort() print data file.close() data = Numeric.array(data) Mehdi On Tue, May 02, 2006 at 03:13:03AM -0400, Barbault Florent florent.barbault:-:paris7.jussieu.fr wrote: > Sent to CCL by: "Barbault Florent" [florent.barbault[A]paris7.jussieu.fr] > > Hi, > > My answer will certainly not please you. I already had this problem of > analysing large energetical data with molecular dynamics simulations. > I think the best solution is to write a software in perl, c or fortran > languages to find the minimum, the maximum and the rms. Your software > will be very quick to find these parameters. The problem will be to > write this program. For your first software you will need long times > for doing it, but it will be very easy for the next. > > Sincerely yours > Florent > > > On Mon, 1 May 2006 08:20:34 -0400 > "Richard L. Wood rwoodphd:msn.com" wrote: > > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > > Hi all, > > > > This question isn't a direct computational chemistry question, but > >an indirect one. So please bear with me. > > > > I'm trying to analyze the output of a 1 nanosecond MD calculation > >that I ran using the program NAMD. Since it's a text file, I could > >use MS Excel to open it and sort the energies from lowest to highest > >value, which is what I would like to do. However, MS Excel has a > >limit of about 65000 lines of text (or rows) that a file can contain. > > Mine has 2000000 lines of text, so that my file is too big. My > >workaround is to open the file in MS Word, and cut it into pieces > >that can be opened in MS Excel. Then I can find the minimum energy > >fro each piece, save that value, and then when done, find the overall > >minimum. Once I've done this, I can find the corresponding frame > >number in the file that contained it, go to the trajectory and save > >those coordinates. > > > > However, as you can imagine, this isn't a very efficient process. > > My simulation takes about 2 and half hours or so to run, while this > >analysis takes about two hours to do. I can therefore do about one > >of these in a day, as I have another non-computational "job" that I > >am doing. At some point, I will be running some smalled > >calculations, which will take much less than two hours to run, and so > >the analysis will take longer than the simulation! > > > > My question is this: does anyone know of a spreadsheat program > >where I can a) import a text file of more than 65000 rows easily, b) > >can sort a given column of that file, and c) works under Windows and > >is free? I've tried Quattro Pro, and all the file comes out in a > >single row! > > > > TIA, > > Richard > > > > > > > > -= This is automatically added to each message by the mailing script > >=- > > To recover the email address of the author of the message, please > >change> Conferences: > >http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >search)> > > From owner-chemistry@ccl.net Tue May 2 07:41:00 2006 From: "Marcin Krol mykrol_._cyf-kr.edu.pl" To: CCL Subject: CCL: help needed Message-Id: <-31651-060502073711-12521-/JcyxNyDOyNqXf9Ij34SvQ#,#server.ccl.net> X-Original-From: Marcin Krol Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 2 May 2006 12:12:38 +0200 (METDST) MIME-Version: 1.0 Sent to CCL by: Marcin Krol [mykrol^cyf-kr.edu.pl] Hi Richard, If you have access to a linux/unix machine try typing this command on the command prompt: grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | tail -1 this should give you the lowest value grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | head -1 this gives you highest value change namd_heat.out to the name of your file. I analyzed an output file > from NAMD 2.5 for Linux-i686-TCP, but I hope that your namd produces an identical file. Namd Total Energy is in column 12, if you want to analyze different quantity (eg. temperature) change $12 to something else. If you don't have access to a linux machine try a script like this in python (I don't know how to install python on windows): import string out_file = open("namd_heat.out",'r') data = out_file.readlines() out_file.close() energy = [] for line in data: try: if line.split()[0] == "ENERGY:": energy.append(eval(line.split()[11])) except: pass energy.sort() print("the lowest energy value is %f\nthe highest energy value is %f\n" %(energy[0], energy[-1])) Hope this helps Marcin On Mon, 1 May 2006, RICHARD JILL WOOD rwoodphd++msn.com wrote: > Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd+*+msn.com] > > > Hi Serena: > > Not to sound lazy, but the problem is that I just don't have the "spare > time" to write code, in unix, or any other language. > > I work five days a week at a low paying non-computational chemistry job, and > I have two days off to work on this project (which I'm not getting > compensated for, obviously) a week, and I'd like to be spending my free time > working on the project, as opposed to writing code for it. I'm hoping to > get this data, package it together with some other calculations that I did > when I was a professional computational chemist, and publish it. > > Obviously, I'm also looking for another computational chemist position. > > So, I'd appreciate any help you can offer. > > Richard > > > >From: "Serena Povia sp422]|[hermes.cam.ac.uk" > >Reply-To: "CCL Subscribers" > >To: "Wood, Richard L. " > >Subject: CCL: help needed > >Date: Mon, 1 May 2006 09:11:09 -0400 > > > >Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk] > >Dear Rich, > > > >I'm sorry to tell you that your problem could be *easily* solved in > >unix, writing a bash/perl script to grep the energy line you're > >interested in some way, and sort them, and go back to pick up the > >energies. It's really a matter of 50 lines of code at > >most and once it's done everything will be authomatic for the following > >calculations. > > > >if you run your calculations on a unix machine you could even run the > >analysis script on it an then get your nice data back in windows. I'm > >learning bash myself and I'll be happy to help. > > > >best, serena > > > > > >On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote: > > > > > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > > > Hi all, > > > > > > This question isn't a direct computational chemistry question, but an > >indirect one. So please bear with me. > > > > > > I'm trying to analyze the output of a 1 nanosecond MD calculation that I > >ran using the program NAMD. Since it's a text file, I could use MS Excel > >to open it and sort the energies from lowest to highest value, which is > >what I would like to do. However, MS Excel has a limit of about 65000 > >lines of text (or rows) that a file can contain. Mine has 2000000 lines of > >text, so that my file is too big. My workaround is to open the file in MS > >Word, and cut it into pieces that can be opened in MS Excel. Then I can > >find the minimum energy fro each piece, save that value, and then when > >done, find the overall minimum. Once I've done this, I can find the > >corresponding frame number in the file that contained it, go to the > >trajectory and save those coordinates. > > > > > > However, as you can imagine, this isn't a very efficient process. My > >simulation takes about 2 and half hours or so to run, while this analysis > >takes about two hours to do. I can therefore do about one of these in a > >day, as I have another non-computational "job" that I am doing. At some > >point, I will be running some smalled calculations, which will take much > >less than two hours to run, and so the analysis will take longer than the > >simulation! > > > > > > My question is this: does anyone know of a spreadsheat program where I > >can a) import a text file of more than 65000 rows easily, b) can sort a > >given column of that file, and c) works under Windows and is free? I've > >tried Quattro Pro, and all the file comes out in a single row! > > > > > > TIA, > > > Richard> > > > > > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today - it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/> > > From owner-chemistry@ccl.net Tue May 2 09:47:00 2006 From: "Phil Hultin hultin- -cc.umanitoba.ca" To: CCL Subject: CCL: Sorting Question Message-Id: <-31652-060502094317-16238-vjSbnOJMTPsHbRdnf1Sn9g(!)server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0046_01C66DC4.72111EA0" Date: Tue, 2 May 2006 08:43:05 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin[a]cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0046_01C66DC4.72111EA0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I have been a bit amused by all the suggestions to help Richard Wood with his question about sorting 2x10^6 lines of text. The majority opinion has been to use some other operating system and to learn a new scripting language. Did nobody actually read Richard's specific statement that he needed something to run under windows, and that was free? I once again point out that windows still contains a perfectly functional command line text sorter (oddly enough, called "SORT"), and it will do exactly what is required using the specified operating system with no more learning than just reading the help file. One line of input required, with arguments to specify the input and output files, and which column of text to sort on, as well as other useful parameters. Nothing against all the suggestions people made - these are very nice ways to do the required task. They just don't meet the customer's specification. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin**cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_0046_01C66DC4.72111EA0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I have been a bit amused by all the suggestions to = help Richard Wood with his question about sorting 2x10^6 lines of = text.

 

The majority opinion has been to use some other = operating system and to learn a new scripting language.  Did nobody actually = read Richard’s specific statement that he needed something to run under windows, and = that was free?

 

I once again point out that windows still contains a perfectly functional command line text sorter (oddly enough, called = “SORT”), and it will do exactly what is required using the specified operating = system with no more learning than just reading the help file.  One line of = input required, with arguments to specify the input and output files, and = which column of text to sort on, as well as other useful = parameters.

 

Nothing against all the suggestions people made = – these are very nice ways to do the required task.  They just = don’t meet the customer’s specification.

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin**cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_0046_01C66DC4.72111EA0-- From owner-chemistry@ccl.net Tue May 2 10:57:00 2006 From: "mehdi.bounouar ~ ch.tum.de (Mehdi Bounouar)" To: CCL Subject: CCL: Sorting Question Message-Id: <-31653-060502102537-11622-LnQr5Pgk1qXtSiQI0Y5rVQ*|*server.ccl.net> X-Original-From: mehdi.bounouar|*|ch.tum.de (Mehdi Bounouar) Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 2 May 2006 16:25:29 +0200 MIME-Version: 1.0 Sent to CCL by: mehdi.bounouar||ch.tum.de (Mehdi Bounouar) > The majority opinion has been to use some other operating system and to > learn a new scripting language. Did nobody actually read Richard's specific > statement that he needed something to run under windows, and that was free? Python runs under Windows and is free :-) > I once again point out that windows still contains a perfectly functional > command line text sorter (oddly enough, called "SORT"), and it will do > exactly what is required using the specified operating system with no more > learning than just reading the help file. One line of input required, with > arguments to specify the input and output files, and which column of text to > sort on, as well as other useful parameters. Well I wonder how many people are still (seriously!!) using command line under under Windows for such purposes (not administration). Mehdi From owner-chemistry@ccl.net Tue May 2 11:32:01 2006 From: "Christopher De Dobbelaere Christopher.DeDobbelaere{=}student.ua.ac.be" To: CCL Subject: CCL:G: increasing NStep for partial optimization Message-Id: <-31654-060502044518-3712-ocJHkatGDOQhb0/7z2zEGA+/-server.ccl.net> X-Original-From: "Christopher De Dobbelaere" Date: Tue, 2 May 2006 04:45:16 -0400 Sent to CCL by: "Christopher De Dobbelaere" [Christopher.DeDobbelaere{:}student.ua.ac.be] Dear ccl members, I'm doing some popt jobs in g03 where the constraint during the optimization is the distance between two molecules. The optimization takes some time and stops after 100 steps. I already increased maxcycles but that just increases the cycles per scf step. Is there a way to increase NStep to a larger value? This is the error i get: Optimization stopped. -- Number of steps exceeded, NStep= 100 -- Flag reset to prevent archiving. This are the options i'm using right now: p b1b95/6-311+G* popt(MaxCyc=250) freq iop(1/8=10) Thanks in advance! Greetings, Christopher Undergrad. Student University of Antwerp From owner-chemistry@ccl.net Tue May 2 12:06:01 2006 From: "Peter Pinski peter.pinski-forum,,web.de" To: CCL Subject: CCL: help needed Message-Id: <-31655-060502105557-14814-s3MeTf3BJvDvEX8NgB5rVw,,server.ccl.net> X-Original-From: Peter Pinski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 02 May 2006 16:55:57 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Pinski [peter.pinski-forum . web.de] Hi, a bourne shell, perl, python etc. run on windows easily using cygwin. (www.cygwin.com) Peter Marcin Krol mykrol_._cyf-kr.edu.pl schrieb: > Sent to CCL by: Marcin Krol [mykrol^cyf-kr.edu.pl] > Hi Richard, > If you have access to a linux/unix machine try typing this command on the > command prompt: > > grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | tail -1 > this should give you the lowest value > > grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | head -1 > this gives you highest value > > change namd_heat.out to the name of your file. I analyzed an output file >> from NAMD 2.5 for Linux-i686-TCP, but I hope that your namd produces an > identical file. Namd Total Energy is in column 12, if you want to analyze > different quantity (eg. temperature) change $12 to something else. > > If you don't have access to a linux machine try a script like this in > python (I don't know how to install python on windows): > > import string > > out_file = open("namd_heat.out",'r') > data = out_file.readlines() > out_file.close() > > energy = [] > for line in data: > try: > if line.split()[0] == "ENERGY:": > energy.append(eval(line.split()[11])) > except: > pass > > energy.sort() > print("the lowest energy value is %f\nthe highest energy value is %f\n" > %(energy[0], energy[-1])) > > Hope this helps > Marcin > > > > On Mon, 1 May 2006, RICHARD JILL WOOD rwoodphd++msn.com wrote: > >> Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd+*+msn.com] >> >> >> Hi Serena: >> >> Not to sound lazy, but the problem is that I just don't have the "spare >> time" to write code, in unix, or any other language. >> >> I work five days a week at a low paying non-computational chemistry job, and >> I have two days off to work on this project (which I'm not getting >> compensated for, obviously) a week, and I'd like to be spending my free time >> working on the project, as opposed to writing code for it. I'm hoping to >> get this data, package it together with some other calculations that I did >> when I was a professional computational chemist, and publish it. >> >> Obviously, I'm also looking for another computational chemist position. >> >> So, I'd appreciate any help you can offer. >> >> Richard >> >> >>> From: "Serena Povia sp422]|[hermes.cam.ac.uk" >>> Reply-To: "CCL Subscribers" >>> To: "Wood, Richard L. " >>> Subject: CCL: help needed >>> Date: Mon, 1 May 2006 09:11:09 -0400 >>> >>> Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk] >>> Dear Rich, >>> >>> I'm sorry to tell you that your problem could be *easily* solved in >>> unix, writing a bash/perl script to grep the energy line you're >>> interested in some way, and sort them, and go back to pick up the >>> energies. It's really a matter of 50 lines of code at >>> most and once it's done everything will be authomatic for the following >>> calculations. >>> >>> if you run your calculations on a unix machine you could even run the >>> analysis script on it an then get your nice data back in windows. I'm >>> learning bash myself and I'll be happy to help. >>> >>> best, serena >>> >>> >>> On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote: >>> >>>> Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] >>>> Hi all, >>>> >>>> This question isn't a direct computational chemistry question, but an >>> indirect one. So please bear with me. >>>> I'm trying to analyze the output of a 1 nanosecond MD calculation that I >>> ran using the program NAMD. Since it's a text file, I could use MS Excel >>> to open it and sort the energies from lowest to highest value, which is >>> what I would like to do. However, MS Excel has a limit of about 65000 >>> lines of text (or rows) that a file can contain. Mine has 2000000 lines of >>> text, so that my file is too big. My workaround is to open the file in MS >>> Word, and cut it into pieces that can be opened in MS Excel. Then I can >>> find the minimum energy fro each piece, save that value, and then when >>> done, find the overall minimum. Once I've done this, I can find the >>> corresponding frame number in the file that contained it, go to the >>> trajectory and save those coordinates. >>>> However, as you can imagine, this isn't a very efficient process. My >>> simulation takes about 2 and half hours or so to run, while this analysis >>> takes about two hours to do. I can therefore do about one of these in a >>> day, as I have another non-computational "job" that I am doing. At some >>> point, I will be running some smalled calculations, which will take much >>> less than two hours to run, and so the analysis will take longer than the >>> simulation! >>>> My question is this: does anyone know of a spreadsheat program where I >>> can a) import a text file of more than 65000 rows easily, b) can sort a >>> given column of that file, and c) works under Windows and is free? I've >>> tried Quattro Pro, and all the file comes out in a single row! >>>> TIA, >>>> Richard> >>> >> _________________________________________________________________ >> Express yourself instantly with MSN Messenger! Download today - it's FREE! >> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/> > > > From owner-chemistry@ccl.net Tue May 2 12:42:01 2006 From: "andras.borosy.:.givaudan.com" To: CCL Subject: CCL:G: PQS ab initio Message-Id: <-31656-060502114034-10106-wFg8JQggROeJHogp6+mtQA^server.ccl.net> X-Original-From: andras.borosy _ givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004DD5E5C1257162_=" Date: Tue, 2 May 2006 16:10:02 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy ~~ givaudan.com This is a multipart message in MIME format. --=_alternative 004DD5E5C1257162_= Content-Type: text/plain; charset="US-ASCII" > Sent to CCL by: "Jim Kress" [ccl_nospam%%kressworks.com] > It's a violation of the (absurd) Gaussian license to perform such a > comparison. If one does such a comparison they will be banned by Gaussian > > from using their software. > > http://www.bannedbygaussian.org/ Which shows that one must not buy Gaussian at all. There are some benchmarks of PQS computations: http://www.pqs-chem.com/benchmarks.shtml Regards, Andras Borosy > > > -----Original Message----- > > From: Debasis Sengupta dxs%%cfdrc.com > > [mailto:owner-chemistry---ccl.net] > > Sent: Friday, April 28, 2006 3:49 PM > > To: Kress, Jim > > Subject: CCL:G: PQS ab initio > > > > Sent to CCL by: Debasis Sengupta [dxs]=[cfdrc.com] Hi, I was > > wondering if anybody has performed any benchmark test on the > > speed of Gaussian 03 and PQS ab initio software (both serial > > and parallel). > > Also I am interested in knowing the experience with PQS from > > those who have used it for a while. > > Thanks > > Debasis > > > > > > > > -= This is automatically added to each message by the mailing > > script =- To recover the email address of the author of the > > message, please change the strange characters on the top line > > to the --- sign. You can also look up the X-Original-From: line > > in the mail header.> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, > > Password: search)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+> > --=_alternative 004DD5E5C1257162_= Content-Type: text/html; charset="US-ASCII"



> Sent to CCL by: "Jim Kress" [ccl_nospam%%kressworks.com]
> It's a violation of the (absurd) Gaussian license to perform such a
> comparison.  If one does such a comparison they will be banned by Gaussian
> > from using their software.
>
> http://www.bannedbygaussian.org/

Which shows that one must not buy Gaussian at all.

There are some benchmarks of PQS computations:

http://www.pqs-chem.com/benchmarks.shtml
Regards,

Andras Borosy

>
> > -----Original Message-----
> > From: Debasis Sengupta dxs%%cfdrc.com
> > [mailto:owner-chemistry---ccl.net]
> > Sent: Friday, April 28, 2006 3:49 PM
> > To: Kress, Jim
> > Subject: CCL:G: PQS ab initio
> >
> > Sent to CCL by: Debasis Sengupta [dxs]=[cfdrc.com] Hi, I was
> > wondering if anybody has performed any benchmark test on the
> > speed of Gaussian 03 and PQS ab initio software (both serial
> > and parallel).
> > Also I am interested in knowing the experience with PQS from
> > those who have used it for a while.
> > Thanks
> > Debasis
> >
> >
> >
> > -= This is automatically added to each message by the mailing
> > script =- To recover the email address of the author of the
> > message, please change the strange characters on the top line
> > to the --- sign. You can also look up the X-Original-From: line
> > in the mail header.> Conferences:
> > http://server.ccl.net/chemistry/announcements/conferences/
> >
> > Search Messages: http://www.ccl.net/htdig  (login: ccl,
> > Password: search)>
> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> > -+-+-+-+-+
> >
> >
> >
> >
> >
> >
>
>
>
>
>
>
>
>
>
>      
>
>
>      
>
>
>      
>
>
>
>
>
>
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
>
>
>      
>
>
>
>
>
>
--=_alternative 004DD5E5C1257162_=-- From owner-chemistry@ccl.net Tue May 2 13:17:00 2006 From: "Peter Pinski peter.pinski-forum\a/web.de" To: CCL Subject: CCL: Sorting Question Message-Id: <-31657-060502114454-17032-gHGqa4PijV0577EZP92P/A++server.ccl.net> X-Original-From: Peter Pinski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 02 May 2006 17:44:59 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Pinski [peter.pinski-forum=-=web.de] Hello, excuse me, if I am wrong. but I have tried the sort function and it seemed that it sorts in an ALPHANUMERICAL order and not in a numerical, i.e. 889<991 but 1021<991 !!! because 1<9. Maybe I have just used the command in a wrong way because I usually use Linux rather than Windows and it really is possible to use dos sort for this job - in this case again I would like to apologise - but I don't think the sort command is the right thing if it makes an output like this: >sort test.txt 1021.02454 890.15454 991.1510 content of test.txt: 890.15454 1021.02454 991.1510 Sincerely, Peter Pinski Phil Hultin hultin- -cc.umanitoba.ca schrieb: > Sent to CCL by: "Phil Hultin" [hultin[a]cc.umanitoba.ca] > This is a multi-part message in MIME format. > > ------=_NextPart_000_0046_01C66DC4.72111EA0 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > I have been a bit amused by all the suggestions to help Richard Wood with > his question about sorting 2x10^6 lines of text. > > > > The majority opinion has been to use some other operating system and to > learn a new scripting language. Did nobody actually read Richard's specific > statement that he needed something to run under windows, and that was free? > > > > I once again point out that windows still contains a perfectly functional > command line text sorter (oddly enough, called "SORT"), and it will do > exactly what is required using the specified operating system with no more > learning than just reading the help file. One line of input required, with > arguments to specify the input and output files, and which column of text to > sort on, as well as other useful parameters. > > > > Nothing against all the suggestions people made - these are very nice ways > to do the required task. They just don't meet the customer's specification. > > > > Dr. Philip G. Hultin > > Associate Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin__cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > > > ------=_NextPart_000_0046_01C66DC4.72111EA0 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> > > > charset=3Dus-ascii"> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"State"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"City"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceName"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceType"/> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"place"/> > > > > > > > >
> >

style=3D'font-size:10.0pt; > font-family:Arial'>I have been a bit amused by all the suggestions to = > help > Richard Wood with his question about sorting 2x10^6 lines of = > text.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>The majority opinion has been to use some other = > operating > system and to learn a new scripting language.  Did nobody actually = > read Richard’s > specific statement that he needed something to run under windows, and = > that was > free?

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>I once again point out that windows still contains a > perfectly functional command line text sorter (oddly enough, called = > “SORT”), > and it will do exactly what is required using the specified operating = > system > with no more learning than just reading the help file.  One line of = > input > required, with arguments to specify the input and output files, and = > which > column of text to sort on, as well as other useful = > parameters.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Nothing against all the suggestions people made = > – > these are very nice ways to do the required task.  They just = > don’t meet > the customer’s specification.

> >

style=3D'font-size:10.0pt; > font-family:Arial'> 

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Dr. Philip G. Hultin

> >

style=3D'font-size:10.0pt; > font-family:Arial'>Associate Professor of = > Chemistry,

> >

u2:st=3D"on"> w:st=3D"on"> = > style=3D'font-size:10.0pt;font-family:Arial'>University 1:PlaceType> size=3D2 face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'> > of w:st=3D"on">Manitoba ace> size=3D2 face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'> >

u2:st=3D"on"> w:st=3D"on"> style=3D'font-size:10.0pt;font-family: > Arial'>Winnipeg face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'>, u2:st=3D"on"> = > w:st=3D"on">MB> size=3D2 face=3DArial> style=3D'font-size:10.0pt;font-family:Arial'> >

style=3D'font-size:10.0pt; > font-family:Arial'>R3T 2N2

> >

style=3D'font-size:10.0pt; > font-family:Arial'> href=3D"mailto:hultin__cc.umanitoba.ca">hultin__cc.umanitoba.ca :p>

> >

style=3D'font-size:10.0pt; > font-family:Arial'> href=3D"http://umanitoba.ca/chemistry/people/hultin">http://umanitoba.ca/= > chemistry/people/hultin

> >

style=3D'font-size: > 12.0pt'> 

> >
> > > > > > ------=_NextPart_000_0046_01C66DC4.72111EA0--> > > > From owner-chemistry@ccl.net Tue May 2 13:52:02 2006 From: "Alain Borel alain.borel|epfl.ch" To: CCL Subject: CCL: help needed Message-Id: <-31658-060502110942-23163-7rEgPLE7azMmAqvxC79B3g,,server.ccl.net> X-Original-From: Alain Borel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 02 May 2006 16:09:26 +0200 MIME-Version: 1.0 Sent to CCL by: Alain Borel [alain.borel:+:epfl.ch] Marcin Krol mykrol_._cyf-kr.edu.pl wrote: > Sent to CCL by: Marcin Krol [mykrol^cyf-kr.edu.pl] > Hi Richard, > If you have access to a linux/unix machine try typing this command on the > command prompt: > > grep "ENERGY:" namd_heat.out | awk '{print $12}' | sort -n -k1 | tail -1 > this should give you the lowest value And if Mr. Wood really wants to go on using Windows, he can use the exact same tools by installing the free Cygwin environment: http://www.cygwin.com Best regards, Alain Borel Bibliothčque Scientifique Commune UNIL-EPFL BCH EPFL - SB - SCGC-BCH 1015 Lausanne, Switzerland. Tel.: +41 21 693 9800 Fax.: +41 21 693 9805 e-mail: alain.borel^_^epfl.ch http://biscom.epfl.ch From owner-chemistry@ccl.net Tue May 2 14:27:00 2006 From: "Ross Walker ross.#%#.rosswalker.co.uk" To: CCL Subject: CCL: AMBER Workshops, London UK 26th - 30th June 2006 Message-Id: <-31659-060502114632-22154-JtA0oc4p6NXAzzogeimbEw#%#server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 2 May 2006 08:46:14 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] Eligibility Note: These workshops are currently open for registration by UK resident academics and students only. A more general registration will be held later if spaces are available. *********************************************************** The EPSRC National Service for Computational Chemistry Software is pleased to announce that it will be holding two workshops on the software package AMBER during the week of the 26th-30th June 2006. The first workshop (26th-27th June) will provide a basic introduction to the software package, while the second workshop (28th-30th June) will be an advanced course specifically geared around the new features in AMBER9. Both workshops will be held in the Chemistry Department at Imperial College London and will be given by Dr Ross Walker (The Scripps Research Institute & San Diego Supercomputer Center), Dr Mike Crowley (The Scripps Research Institute) and Dr Ian Gould (Imperial College London). Professor David Case (The Scripps Research Institute) will also be a tutor at the advanced workshop. AMBER is a software package for applying molecular mechanics, molecular dynamics and free energy calculations to simulate biomolecules. The workshops will consist of a series of short lectures followed by hands-on lab sessions that will cover use of the AMBER molecular dynamics software suite (http://amber.scripps.edu) and the theory behind it. There will also be opportunities for one-to- one discussions with the tutors for advice with specific research problems. Specific topics to be covered in each of the workshops are summarised below. Eligibility and Registration The workshops are open to all users and potential users of our service, and both academic staff and students in the UK are welcome. Registration is free but participants are expected to pay for their own travel and accommodation. Users may choose to register for one or both courses, but should be aware that the advanced course is really only suitable for people who have at least some background in molecular dynamics simulations. The deadline for all applications is Friday 9th June 2006. Application forms can be downloaded from the NSCCS website at: http://www.nsccs.ac.uk/amber_workshop2006.php Queries about either workshop should be sent by email to sarah.wilsey- -imperial.ac.uk. AMBER Basic Training Workshop: 26th - 27th June 2006 - An introduction to modelling and the principles of classical molecular dynamics including minimisation and dynamics algorithms, temperature regulation, pressure regulation and periodic boundary methods; implicit and explicit solvation models; the limitations of using a classical approach. - An introduction to each of the modules that make up the AMBER software suite, and a description of each of the different parameter sets available, the pros and cons of each and where to obtain help. - "Simple" peptide, protein and nucleic acid simulations including how to obtain a starting structure, creating prmtop and inpcrd files, running minimisations, gas phase and implicit solvent molecular dynamics, and how to view and analyse the results. - More advanced simulations of co-enzyme containing proteins and pharmaceutical compounds that require explicit parameters; how to create your own residues, including charge derivation and parameter selection. - An introduction to QM/MM coupled potential simulations. AMBER Advanced Training Workshop: 28th - 30th June 2006 - Solvation Energy Calculations with MMPBSA. - Advanced trajectory analysis (clustering, H-bond analysis, correlation functions...). - Reaction free energies with Thermodynamic Integration. - Reaction pathway sampling with QM/MM and nudged elastic band. - Replica Exchange MD. - Empirical Valence Bond Calculations. - Constant pH MD. - Considerations for setting up non-standard molecules. (Charge Derivation with R.E.D. and parameter selection). - Consideration for running simulations on parallel computers. Cluster design, bottlenecks, performance improvement, introduction to running simulations on supercomputers. - A selection of the most requested topics by applicants. *********************************************************** /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross- -rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Tue May 2 15:01:00 2006 From: "Richard W Harper HARPER_RICHARD_W#Lilly.com" To: CCL Subject: CCL: Sorting in Windows Message-Id: <-31660-060502115655-27424-HQyK4GEczfKa1k8lnUtAlQ=-=server.ccl.net> X-Original-From: Richard W Harper Content-return: prohibited Content-type: multipart/alternative; boundary="=_alternative 0050B70285257162_=" Date: Tue, 02 May 2006 10:41:37 -0400 MIME-version: 1.0 Sent to CCL by: Richard W Harper [HARPER_RICHARD_W..Lilly.com] This is a multipart message in MIME format. --=_alternative 0050B70285257162_= Content-Type: text/plain; charset="US-ASCII" Thanks for the tip regarding windows "sort". I would also like to point out that there are windows versions of perl, python and probably other scripting languages that would be suitable for attacking similar problems that are not as easily solved. Pardon me if someone already suggested this and I missed it. Richard W. Harper Computational Chemist Lilly Research Laboratories --=_alternative 0050B70285257162_= Content-Type: text/html; charset="US-ASCII"
Thanks for the tip regarding windows "sort".  I would also like to point out that there are windows versions of perl, python and probably other scripting languages that would be suitable for attacking similar problems that are not as easily solved.  Pardon me if someone already suggested this and I missed it.

Richard W. Harper
Computational Chemist
Lilly Research Laboratories --=_alternative 0050B70285257162_=-- From owner-chemistry@ccl.net Tue May 2 15:37:08 2006 From: "Shobe, David dshobe[*]sud-chemieinc.com" To: CCL Subject: CCL: Sorting Question Message-Id: <-31661-060502122651-14466-l0o1/zYzWwGvVfzY6L4t+Q a server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 2 May 2006 18:26:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe]=[sud-chemieinc.com] There is a Windows version of Perl, and it is free, so those answers were not entirely off topic. The issue here may be whether Dr. Wood already knows Perl or a similar scripting language. As has been pointed out, *writing* the script can be done in under 10 minutes. *Learning* the language, especially if it is your first programming language, is very time consuming. OTOH, if the DOS sort command works for him, there's no need for anything more complicated. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry#,#ccl.net [mailto:owner-chemistry#,#ccl.net] Sent: Tuesday, May 02, 2006 9:54 AM To: Shobe, David Subject: CCL: Sorting Question Sent to CCL by: "Phil Hultin" [hultin[a]cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0046_01C66DC4.72111EA0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I have been a bit amused by all the suggestions to help Richard Wood with his question about sorting 2x10^6 lines of text. The majority opinion has been to use some other operating system and to learn a new scripting language. Did nobody actually read Richard's specific statement that he needed something to run under windows, and that was free? I once again point out that windows still contains a perfectly functional command line text sorter (oddly enough, called "SORT"), and it will do exactly what is required using the specified operating system with no more learning than just reading the help file. One line of input required, with arguments to specify the input and output files, and which column of text to sort on, as well as other useful parameters. Nothing against all the suggestions people made - these are very nice ways to do the required task. They just don't meet the customer's specification. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin__cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_0046_01C66DC4.72111EA0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I have been a bit amused by all the suggestions to = help Richard Wood with his question about sorting 2x10^6 lines of = text.

 

The majority opinion has been to use some other = operating system and to learn a new scripting language.  Did nobody actually = read Richard’s specific statement that he needed something to run under windows, and = that was free?

 

I once again point out that windows still contains a perfectly functional command line text sorter (oddly enough, called = “SORT”), and it will do exactly what is required using the specified operating = system with no more learning than just reading the help file.  One line of = input required, with arguments to specify the input and output files, and = which column of text to sort on, as well as other useful = parameters.

 

Nothing against all the suggestions people made = – these are very nice ways to do the required task.  They just = don’t meet the customer’s specification.

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin__cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_0046_01C66DC4.72111EA0--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue May 2 16:12:00 2006 From: "Shobe, David dshobe!^!sud-chemieinc.com" To: CCL Subject: CCL: Sorting Question Message-Id: <-31662-060502123107-19903-jJeaYDk1EF2KHbBnoRYBSw+*+server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 2 May 2006 18:30:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe/a\sud-chemieinc.com] Sent to CCL by: mehdi.bounouar||ch.tum.de (Mehdi Bounouar): Well I wonder how many people are still (seriously!!) using command line under under Windows for such purposes (not administration). But if it's *there* and he already has it, why shouldn't he use it? --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. This e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Tue May 2 16:47:01 2006 From: "John McKelvey jmmckel-,-attglobal.net" To: CCL Subject: CCL: Sorting Question Message-Id: <-31663-060502115431-26372-VnuubneqKp0u71cLiWQJbA*|*server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 May 2006 11:47:12 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|-|attglobal.net] >Well I wonder how many people are still (seriously!!) using command line >under under Windows for such purposes (not administration). > > > With no intention of throwing rocks, I recall getting chastised in grad school for not trying the easy solution first... Cheers.. John McKelvey > > From owner-chemistry@ccl.net Tue May 2 17:22:00 2006 From: "Ioana Cozmuta icozmuta]^[mail.arc.nasa.gov" To: CCL Subject: CCL: help needed Message-Id: <-31664-060502021350-32473-Gm9TXRY9fCMIhXZ//7tUjg|server.ccl.net> X-Original-From: Ioana Cozmuta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 01 May 2006 22:14:32 -0700 MIME-Version: 1.0 Sent to CCL by: Ioana Cozmuta [icozmuta^^^mail.arc.nasa.gov] Hi Richard, Do you have access to a unix terminal? Please let me know. if so then I can send you a short shell/cshell script that does what you want and should solve your problem in minutes. From what i understand from your e-mail you are using a windows machine(??). If you have cygwin on windows (that is a free software) that could be also a possibility as cygwin emulates a unix environment. If you have a Mac then you are lucky... Let me know what systems you have access to and if you could use a shell script. Best, Ioana RICHARD JILL WOOD rwoodphd++msn.com wrote: > Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd+*+msn.com] > > > Hi Serena: > > Not to sound lazy, but the problem is that I just don't have the "spare > time" to write code, in unix, or any other language. > > I work five days a week at a low paying non-computational chemistry job, and > I have two days off to work on this project (which I'm not getting > compensated for, obviously) a week, and I'd like to be spending my free time > working on the project, as opposed to writing code for it. I'm hoping to > get this data, package it together with some other calculations that I did > when I was a professional computational chemist, and publish it. > > Obviously, I'm also looking for another computational chemist position. > > So, I'd appreciate any help you can offer. > > Richard > > > >> From: "Serena Povia sp422]|[hermes.cam.ac.uk" >> Reply-To: "CCL Subscribers" >> To: "Wood, Richard L. " >> Subject: CCL: help needed >> Date: Mon, 1 May 2006 09:11:09 -0400 >> >> Sent to CCL by: Serena Povia [sp422(_)hermes.cam.ac.uk] >> Dear Rich, >> >> I'm sorry to tell you that your problem could be *easily* solved in >> unix, writing a bash/perl script to grep the energy line you're >> interested in some way, and sort them, and go back to pick up the >> energies. It's really a matter of 50 lines of code at >> most and once it's done everything will be authomatic for the following >> calculations. >> >> if you run your calculations on a unix machine you could even run the >> analysis script on it an then get your nice data back in windows. I'm >> learning bash myself and I'll be happy to help. >> >> best, serena >> >> >> On Mon, 1 May 2006, Richard L. Wood rwoodphd:msn.com wrote: >> >> >>> Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] >>> Hi all, >>> >>> This question isn't a direct computational chemistry question, but an >>> >> indirect one. So please bear with me. >> >>> I'm trying to analyze the output of a 1 nanosecond MD calculation that I >>> >> ran using the program NAMD. Since it's a text file, I could use MS Excel >> to open it and sort the energies from lowest to highest value, which is >> what I would like to do. However, MS Excel has a limit of about 65000 >> lines of text (or rows) that a file can contain. Mine has 2000000 lines of >> text, so that my file is too big. My workaround is to open the file in MS >> Word, and cut it into pieces that can be opened in MS Excel. Then I can >> find the minimum energy fro each piece, save that value, and then when >> done, find the overall minimum. Once I've done this, I can find the >> corresponding frame number in the file that contained it, go to the >> trajectory and save those coordinates. >> >>> However, as you can imagine, this isn't a very efficient process. My >>> >> simulation takes about 2 and half hours or so to run, while this analysis >> takes about two hours to do. I can therefore do about one of these in a >> day, as I have another non-computational "job" that I am doing. At some >> point, I will be running some smalled calculations, which will take much >> less than two hours to run, and so the analysis will take longer than the >> simulation! >> >>> My question is this: does anyone know of a spreadsheat program where I >>> >> can a) import a text file of more than 65000 rows easily, b) can sort a >> given column of that file, and c) works under Windows and is free? I've >> tried Quattro Pro, and all the file comes out in a single row! >> >>> TIA, >>> Richard> >>> >> > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! Download today - it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/> > > > > -- Ioana Cozmuta, Ph.D Eloret Corporation NASA Ames Research Center Mail Stop 230-3 Moffett Field, CA 94035 phone (650) 604-0993 e-mail: icozmuta/a\mail.arc.nasa.gov http://people.nas.nasa.gov/~ioana/ From owner-chemistry@ccl.net Tue May 2 17:57:01 2006 From: "Dr. N. SUKUMAR nagams**rpi.edu" To: CCL Subject: CCL: help needed Message-Id: <-31665-060502133258-27231-CE/tPBtwoDgvFNSwERF6Pw(-)server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Tue, 02 May 2006 13:32:53 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams^_^rpi.edu] This discussion brings out several curious features about scientific practice today: On the one hand, we have some who would rather spend hours cutting and pasting between Word and Excel (with who knows how many mistakes in the process) than spend the time to write 5 lines of perl/python/DOS/bash-under-Cygwin Script to do the job once and forever. On the other hand, the suggestion to use a DOS command is criticized because no one uses command line DOS anymore. Of course, that is SUCH a good reason. Yes, I know lots of lay people (using computers for email) who would have a heart attack at the mere thought of opening up that little black box known as the command prompt, but here?? on CCL? Rather spend hours with InstallShieldWizard and rebooting multiple times than open up that little black box? At the same time, those who suggested perl/python scripts (all of which run under Windows) are criticized because this is not what the "customer" asked for. Well, if it was a paying customer, this makes sense and that would be the end of that. But here it is a fellow scientist seeking ADVICE, not a customer demanding a specific PRODUCT. If folks are approaching CCL as customers trying to get products for free, there's no reason for the rest of us to be volunteering time and expertise here. There are multiple ways of getting most jobs done and opinions will always differ on the relative merits of different strategies, depending upon our specific requirements and individual expertise and constraints. Being exposed to multiple strategies is what enables each of us to make an informed choice specific to our circumstances. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Tue May 2 18:32:01 2006 From: "Charles McCallum mmccallum]|[pacific.edu" To: CCL Subject: CCL: help needed Message-Id: <-31666-060502092921-14748-yWtOyDdA+jwqrcRGcaCv2Q\a/server.ccl.net> X-Original-From: Charles McCallum Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 2 May 2006 06:29:03 -0700 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Charles McCallum [mmccallum|-|pacific.edu] I'd also chime in here and say do it in perl or python or.... The amount of time you will fight with excel or whatever is not at all worth it, and if you learn even a little bit of perl (or python or...), you will be able to do things on the fly whenever it is called for. I recently thought that Excel would do such a chore for me, especially since my wife is in business and is an excel whiz (thought she could help); No go. Excel simply can't program in the flexible way that perl can. I had to learn some new perl constructs (my perl is/was extremely rusty), but in an hour or two, the complex sorting was done, and since I did this with a student, he understands the programming to. As others have said, not the answer you wanted to hear, but perhaps the best solution overall. Cheers, Mike On May 1, 2006, at 5:22 AM, Richard L. Wood rwoodphd:msn.com wrote: > Sent to CCL by: "Richard L. Wood" [rwoodphd##msn.com] > Hi all, > > This question isn't a direct computational chemistry question, but > an indirect one. So please bear with me. > > I'm trying to analyze the output of a 1 nanosecond MD calculation > that I ran using the program NAMD. Since it's a text file, I could > use MS Excel to open it and sort the energies from lowest to > highest value, which is what I would like to do. However, MS Excel > has a limit of about 65000 lines of text (or rows) that a file can > contain. Mine has 2000000 lines of text, so that my file is too > big. My workaround is to open the file in MS Word, and cut it into > pieces that can be opened in MS Excel. Then I can find the minimum > energy fro each piece, save that value, and then when done, find > the overall minimum. Once I've done this, I can find the > corresponding frame number in the file that contained it, go to the > trajectory and save those coordinates. > > However, as you can imagine, this isn't a very efficient process. > My simulation takes about 2 and half hours or so to run, while this > analysis takes about two hours to do. I can therefore do about one > of these in a day, as I have another non-computational "job" that I > am doing. At some point, I will be running some smalled > calculations, which will take much less than two hours to run, and > so the analysis will take longer than the simulation! > > My question is this: does anyone know of a spreadsheat program > where I can a) import a text file of more than 65000 rows easily, > b) can sort a given column of that file, and c) works under Windows > and is free? I've tried Quattro Pro, and all the file comes out in > a single row! > > TIA, > Richard > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- C. Michael McCallum http://www.pacific.edu/college/ chemistry/McCallum/cmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax From owner-chemistry@ccl.net Tue May 2 19:07:01 2006 From: "Xiaobo Zheng xiaoboccl:+:gmail.com" To: CCL Subject: CCL:G: Cartesian Coordinate Transformation Message-Id: <-31667-060502145741-19614-oxzWI6VJQ25Cnz1W013ekw(0)server.ccl.net> X-Original-From: "Xiaobo Zheng" Date: Tue, 2 May 2006 14:57:39 -0400 Sent to CCL by: "Xiaobo Zheng" [xiaoboccl#%#gmail.com] Dear CCLer, I am using Gaussian to optimized geometries with constraints and my input format is in cartesian coordinate. But after optimization, somtimes, Gaussian output does not contain my original cartesian coordinate information. Instead, it reports "standard orientation", which is a transformation of my original coordinate. I am just wondering if there is an easy way or tools to transform Gaussian "starndard orientation" back to my cartesian coordinate. Thanks for your input. Xiaobo Zheng From owner-chemistry@ccl.net Tue May 2 19:42:00 2006 From: "Phil Hultin hultin*|*cc.umanitoba.ca" To: CCL Subject: CCL: Sorting Question Message-Id: <-31668-060502151254-2669-mv3ZBuBP7WDoYcWrkCQ2MA-#-server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01C66DF2.7D1D8E40" Date: Tue, 2 May 2006 14:12:41 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin__cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C66DF2.7D1D8E40 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I certainly do not want to defend Windows! >Peter Pinski [peter.pinski-forum=-=web.de] Hello, > >excuse me, if I am wrong. but I have tried the sort function and it seemed that it sorts in an >ALPHANUMERICAL order and not in a numerical, i.e. 889<991 but 1021<991 !!! because 1<9. Peter is correct, the DOS sort does use alphanumerical order, which is kind of stupid, but not a serious problem provided that the data is in the appropriate format. INPUT FILE: test.txt first 123.456 second 987.654 third 1234.56 fourth 9.87654 sort test.txt /+11 /O testsort.txt OUTPUT FILE: testsort.txt fourth 9.87654 first 123.456 second 987.654 third 1234.56 In other words, the data has to be decimal aligned and you need to tell the sort where the beginning of the numeric field is. This however, will encounter some problems with scientific notation unless it is expressed carefully. So, in conclusion, perhaps there are drawbacks to the Windows solution and it may indeed be worthwhile downloading, installing and learning a new command environment - but let's not forget that simple is usually better than complex for the end user. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin-,-cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_0014_01C66DF2.7D1D8E40 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I certainly do not want to defend = Windows!

 

>Peter Pinski [peter.pinski-forum=3D-=3Dweb.de] Hello,

> 

>excuse me, if I am wrong. but I have tried the sort function and it seemed that it = sorts in an >ALPHANUMERICAL order and not in a numerical, i.e. 889<991 but 1021<991 !!! because 1<9.

 

Peter is correct, the DOS sort does use = alphanumerical order, which is kind of stupid, but not a serious problem provided that = the data is in the appropriate format.

 

INPUT FILE: = test.txt

first      123.456

second     987.654

third     1234.56

fourth       9.87654

 

sort test.txt /+11 /O = testsort.txt

 

OUTPUT FILE: = testsort.txt

fourth       9.87654

first      123.456

second     987.654

third     1234.56

 

In other words, the data has to be decimal = aligned and you need to tell the sort where the beginning of the numeric field = is.  This however, will encounter some problems with scientific notation unless it = is expressed carefully.

 

So, in conclusion, perhaps there are drawbacks = to the Windows solution and it may indeed be worthwhile downloading, installing = and learning a new command environment – but let’s not forget = that simple is usually better than complex for the end = user.

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin-,-cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_0014_01C66DF2.7D1D8E40-- From owner-chemistry@ccl.net Tue May 2 20:17:04 2006 From: "Dr. N. SUKUMAR nagams-.-rpi.edu" To: CCL Subject: CCL:G: increasing NStep for partial optimization Message-Id: <-31669-060502155407-29518-Qx/8eilJSJNHhUaJwHX+eQ::server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Tue, 02 May 2006 15:54:00 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams_._rpi.edu] ==============Original message text=============== On Tue, 02 May 2006 11:46:39 EDT "Christopher De Dobbelaere Christopher.DeDobbelaere{=}student.ua.ac.be" wrote: Sent to CCL by: "Christopher De Dobbelaere" [Christopher.DeDobbelaere{:}student.ua.ac.be] Dear ccl members, I'm doing some popt jobs in g03 where the constraint during the optimization is the distance between two molecules. The optimization takes some time and stops after 100 steps. I already increased maxcycles but that just increases the cycles per scf step. Is there a way to increase NStep to a larger value? This is the error i get: Optimization stopped. -- Number of steps exceeded, NStep= 100 -- Flag reset to prevent archiving. This are the options i'm using right now: p b1b95/6-311+G* popt(MaxCyc=250) freq iop(1/8=10) Thanks in advance! Greetings, Christopher Undergrad. Student University of Antwerp ===========End of original message text=========== There is a MaxCycle keyword for both the OPT and the SCF procedures. To increase the number of optimization steps, use: Opt=(MaxCycle=N) where N is the desired maximum number of optimization steps. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Tue May 2 20:52:00 2006 From: "Geoffrey Hutchison grh25|a|cornell.edu" To: CCL Subject: CCL: Sorting Question Message-Id: <-31670-060502142349-27542-KaVt0Y9vNJpax9YafbUPGQ:_:server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 2 May 2006 14:23:33 -0400 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Geoffrey Hutchison [grh25(a)cornell.edu] > Maybe I have just used the command in a wrong way because I usually > use > Linux rather than Windows I don't know DOS. But to answer your point, if you wish to sort numeric data on Linux or a UNIX platform (e.g., Solaris, Mac OS X...) sort -n data.txt The "-n" flag sorts data using a numeric comparison. If you want a reverse sort (e.g., large numbers up top) sort -rn data.txt As several people have pointed out, command-line utilities (whether DOS, Windows, UNIX, Linux...) can be *very* useful for streamlining computational chemistry tasks. They're often designed for huge data sets. Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruńa Group http://abruna.chem.cornell.edu/ From owner-chemistry@ccl.net Tue May 2 21:27:02 2006 From: "Peter Pinski peter.pinski-forum- -web.de" To: CCL Subject: CCL: Sorting Question Message-Id: <-31671-060502172934-9534-qi1ge2ZI+DZPzU53kGFffg=-=server.ccl.net> X-Original-From: Peter Pinski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 02 May 2006 23:29:39 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Pinski [peter.pinski-forum],[web.de] Hi, I don't know, whether there are different sort versions in different windows versions, but e.g. on windows xp the sort command, as I already have pointed out once, SHOULD NOT work because it sorts alphanumerically and not numerically. In plain speach, 1000 is for the ms dos sort smaller than 900! Of course it's not neccessary to program perl or python or whatever for doing this task. As also already has been mentioned, an alternative is the unix sort command, which is able to sort numerically if invoked with the -g flag. It's possible to specify a field with the -k flag. The unix sort for windows may either be used by installing cygwin or installing the gnu textutils for windows available at http://gnuwin32.sourceforge.net/packages/textutils.htm I may be started in a dos box. For a list of flags see sort --help. Maybe it's necessary to rename the file sort.exe in order to avoid a conflict with the windows sort. Again, maybe there are different versions of ms dos sort, but those I have seen yet will provide wrong results because they sort alphanumerically rather than numerically. Greetings, Peter Pinski John McKelvey jmmckel-,-attglobal.net schrieb: > Sent to CCL by: John McKelvey [jmmckel|-|attglobal.net] > >> Well I wonder how many people are still (seriously!!) using command line >> under under Windows for such purposes (not administration). >> >> >> > With no intention of throwing rocks, I recall getting chastised in grad > school for not trying the easy solution first... > > Cheers.. > John McKelvey> > > > From owner-chemistry@ccl.net Tue May 2 22:01:01 2006 From: "Serena Povia sp422(~)hermes.cam.ac.uk" To: CCL Subject: CCL: help needed << out of hand? Message-Id: <-31672-060502184018-27759-fh1ZCi+j4gZsvO4qTr/p7w,+,server.ccl.net> X-Original-From: Serena Povia Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 2 May 2006 23:40:08 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Serena Povia [sp422.!^!.hermes.cam.ac.uk] Ok, the thread went slightly out of hand. The poor Rich will have an heart attack checking the email after a dreadful non-CC-working day, for how many ppl are arguing on his innocent sorting help request. We have several point of view, linux geeks (in which I'm trying to sneak in), allergic to the evilness of Win, Win users who riesumate dusty, yet useful, DOS commands, being told off by the penguin lovers. Equilibrated ppl suggested a bash simulator, which I appreciated a lot. Nevertheless the discussion seems to be spiraling down as a contrapposition of different churches. lol My opinion might biased but I suggest that we all wait for Rich's reply, before going ahead on discussing the undoubtable advantages of what we believe in (the penguin? or the Gates?) Rich, any feedback? warmest regards, Serena On Tue, 2 May 2006, Dr. N. SUKUMAR nagams**rpi.edu wrote: > Sent to CCL by: "Dr. N. SUKUMAR" [nagams^_^rpi.edu] > This discussion brings out several curious features about scientific > practice today: > > On the one hand, we have some who would rather spend hours cutting and > pasting between Word and Excel (with who knows how many mistakes in the > process) than spend the time to write 5 lines of > perl/python/DOS/bash-under-Cygwin Script to do the job once and forever. > > On the other hand, the suggestion to use a DOS command is criticized > because no one uses command line DOS anymore. Of course, that is SUCH a > good reason. Yes, I know lots of lay people (using computers for email) > who would have a heart attack at the mere thought of opening up that > little black box known as the command prompt, but here?? on CCL? Rather > spend hours with InstallShieldWizard and rebooting multiple times than > open up that little black box? > > At the same time, those who suggested perl/python scripts (all of which > run under Windows) are criticized because this is not what the "customer" > asked for. Well, if it was a paying customer, this makes sense and that > would be the end of that. But here it is a fellow scientist seeking > ADVICE, not a customer demanding a specific PRODUCT. If folks are > approaching CCL as customers trying to get products for free, there's no > reason for the rest of us to be volunteering time and expertise here. > > There are multiple ways of getting most jobs done and opinions will > always differ on the relative merits of different strategies, depending > upon our specific requirements and individual expertise and constraints. > Being exposed to multiple strategies is what enables each of us to make > an informed choice specific to our circumstances. > > Dr. N. Sukumar > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute> > > > From owner-chemistry@ccl.net Tue May 2 22:37:00 2006 From: "Gustavo Mercier gamercier,+,yahoo.com" To: CCL Subject: CCL: Sorting Question Message-Id: <-31673-060502155519-32214-Q0/ba8ktyANAsLcovOkC6g a server.ccl.net> X-Original-From: Gustavo Mercier Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-898632598-1146596113=:39457" Date: Tue, 2 May 2006 11:55:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier ~ yahoo.com] --0-898632598-1146596113=:39457 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi! I had the same experience using the dos sort function. I tried the help facility and it did not specify a switch to do a numeric sort. The gnu sort function is more flexible. I think the need to process large files in an efficient fashion is a perfect illustration why command line interfaces are not obsolete. It is time well spent for those working in CC to learn a scripting language. There are many options, even for those working under windows. Learn one well and it will be a nice addition to your toolbox. Bye! GM "Peter Pinski peter.pinski-foruma/web.de" wrote: Sent to CCL by: Peter Pinski [peter.pinski-forum=-=web.de] Hello, excuse me, if I am wrong. but I have tried the sort function and it seemed that it sorts in an ALPHANUMERICAL order and not in a numerical, i.e. 889<991 but 1021<991 !!! because 1<9. Maybe I have just used the command in a wrong way because I usually use Linux rather than Windows and it really is possible to use dos sort for this job - in this case again I would like to apologise - but I don't think the sort command is the right thing if it makes an output like this: >sort test.txt 1021.02454 890.15454 991.1510 content of test.txt: 890.15454 1021.02454 991.1510 Sincerely, Peter Pinski Phil Hultin hultin- -cc.umanitoba.ca schrieb: > Sent to CCL by: "Phil Hultin" [hultin[a]cc.umanitoba.ca] > This is a multi-part message in MIME format. > > ------=_NextPart_000_0046_01C66DC4.72111EA0 > Content-Type: text/plain; > charset="us-ascii" > Content-Transfer-Encoding: 7bit > > I have been a bit amused by all the suggestions to help Richard Wood with > his question about sorting 2x10^6 lines of text. > > > > The majority opinion has been to use some other operating system and to > learn a new scripting language. Did nobody actually read Richard's specific > statement that he needed something to run under windows, and that was free? > > > > I once again point out that windows still contains a perfectly functional > command line text sorter (oddly enough, called "SORT"), and it will do > exactly what is required using the specified operating system with no more > learning than just reading the help file. One line of input required, with > arguments to specify the input and output files, and which column of text to > sort on, as well as other useful parameters. > > > > Nothing against all the suggestions people made - these are very nice ways > to do the required task. They just don't meet the customer's specification. > > > > Dr. Philip G. Hultin > > Associate Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin__cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > > > ------=_NextPart_000_0046_01C66DC4.72111EA0 > Content-Type: text/html; > charset="us-ascii" > Content-Transfer-Encoding: quoted-printable > > > xmlns:o=3D"urn:schemas-microsoft-com:office:office" = > xmlns:w=3D"urn:schemas-microsoft-com:office:word" = > xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" = > xmlns=3D"http://www.w3.org/TR/REC-html40"> > > > > charset=3Dus-ascii"> > > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"State"/> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"City"/> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceName"/> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"PlaceType"/> > > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags" > name=3D"place"/> > > > st1\:*{behavior:url(#default#ieooui) } > > > > > /* Font Definitions */ > __font-face > {font-family:Times; > panose-1:2 2 6 3 5 4 5 2 3 4;} > /* Style Definitions */ > p.MsoNormal, li.MsoNormal, div.MsoNormal > {margin:0in; > margin-bottom:.0001pt; > font-size:12.0pt; > font-family:"Times New Roman";} > p.MsoTitle, li.MsoTitle, div.MsoTitle > {margin-top:12.0pt; > margin-right:0in; > margin-bottom:3.0pt; > margin-left:0in; > text-align:center; > font-size:16.0pt; > font-family:Arial; > font-weight:bold;} > p.MsoClosing, li.MsoClosing, div.MsoClosing > {margin-top:12.0pt; > margin-right:0in; > margin-bottom:48.0pt; > margin-left:3.0in; > font-size:12.0pt; > font-family:"Times New Roman";} > p.MsoSignature, li.MsoSignature, div.MsoSignature > {margin-top:0in; > margin-right:0in; > margin-bottom:6.0pt; > margin-left:3.0in; > font-size:12.0pt; > font-family:"Times New Roman";} > p.MsoBodyText, li.MsoBodyText, div.MsoBodyText > {margin-top:0in; > margin-right:0in; > margin-bottom:6.0pt; > margin-left:0in; > font-size:12.0pt; > font-family:"Times New Roman";} > p.MsoSalutation, li.MsoSalutation, div.MsoSalutation > {margin-top:0in; > margin-right:0in; > margin-bottom:6.0pt; > margin-left:0in; > font-size:12.0pt; > font-family:"Times New Roman";} > p.MsoBodyTextFirstIndent, li.MsoBodyTextFirstIndent, = > div.MsoBodyTextFirstIndent > {margin-top:0in; > margin-right:0in; > margin-bottom:6.0pt; > margin-left:0in; > text-indent:10.5pt; > font-size:12.0pt; > font-family:"Times New Roman";} > a:link, span.MsoHyperlink > {color:blue; > text-decoration:underline;} > a:visited, span.MsoHyperlinkFollowed > {color:purple; > text-decoration:underline;} > span.Strikeout > {color:red; > text-decoration:line-through;} > p.Title2, li.Title2, div.Title2 > {margin-top:12.0pt; > margin-right:0in; > margin-bottom:6.0pt; > margin-left:0in; > text-align:center; > font-size:24.0pt; > font-family:"Times New Roman"; > font-weight:bold;} > span.EmailStyle25 > {mso-style-type:personal-compose; > font-family:Arial; > color:windowtext;} > __page Section1 > {size:8.5in 11.0in; > margin:1.0in 1.25in 1.0in 1.25in;} > div.Section1 > {page:Section1;} > --> > > > > > > > > > > > > > > > style=3D'font-size:10.0pt; > font-family:Arial'>I have been a bit amused by all the suggestions to = > help > Richard Wood with his question about sorting 2x10^6 lines of = > text. > > > style=3D'font-size:10.0pt; > font-family:Arial'> > > > style=3D'font-size:10.0pt; > font-family:Arial'>The majority opinion has been to use some other = > operating > system and to learn a new scripting language. Did nobody actually = > read Richard’s > specific statement that he needed something to run under windows, and = > that was > free? > > > style=3D'font-size:10.0pt; > font-family:Arial'> > > > style=3D'font-size:10.0pt; > font-family:Arial'>I once again point out that windows still contains a > perfectly functional command line text sorter (oddly enough, called = > “SORT”), > and it will do exactly what is required using the specified operating = > system > with no more learning than just reading the help file. One line of = > input > required, with arguments to specify the input and output files, and = > which > column of text to sort on, as well as other useful = > parameters. > > > style=3D'font-size:10.0pt; > font-family:Arial'> > > > style=3D'font-size:10.0pt; > font-family:Arial'>Nothing against all the suggestions people made = > – > these are very nice ways to do the required task. They just = > don’t meet > the customer’s specification. > > > style=3D'font-size:10.0pt; > font-family:Arial'> > > > style=3D'font-size:10.0pt; > font-family:Arial'>Dr. Philip G. Hultin > > > style=3D'font-size:10.0pt; > font-family:Arial'>Associate Professor of = > Chemistry, > > > u2:st=3D"on"> > w:st=3D"on"> > = > style=3D'font-size:10.0pt;font-family:Arial'>University > 1:PlaceType> > size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'> > of > w:st=3D"on">Manitoba > ace> > size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'> > > > u2:st=3D"on"> > w:st=3D"on">> style=3D'font-size:10.0pt;font-family: > Arial'>Winnipeg> face=3DArial> > style=3D'font-size:10.0pt;font-family:Arial'>, > u2:st=3D"on"> > = > w:st=3D"on">MB >> > size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'> > > > style=3D'font-size:10.0pt; > font-family:Arial'>R3T 2N2 > > > style=3D'font-size:10.0pt; > font-family:Arial'>> href=3D"mailto:hultin__cc.umanitoba.ca">hultin__cc.umanitoba.ca > :p> > > > style=3D'font-size:10.0pt; > font-family:Arial'>> href=3D"http://umanitoba.ca/chemistry/people/hultin">http://umanitoba.ca/= > chemistry/people/hultin > > > style=3D'font-size: > 12.0pt'> > > > > > > > > ------=_NextPart_000_0046_01C66DC4.72111EA0--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Gustavo A. Mercier, Jr. MD,PhD Baylor University Medical Center Radiology American Radiology Associates 712 N. Washington, Suite 101 Dallas, TX 75246 214-826-8822 214-826-9792 fax gamercier^^^yahoo.com --0-898632598-1146596113=:39457 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi!

I had the same experience using the dos sort function. I tried the help facility and it did not specify a switch to do a numeric sort. The gnu sort function is more flexible. I think the need to process large files in an efficient fashion is a perfect illustration why command line interfaces are not obsolete. It is time well spent for those working in CC to learn a scripting language. There are many options, even for those working under windows. Learn one well and it will be a nice addition to your toolbox.

Bye!
GM

"Peter Pinski peter.pinski-foruma/web.de" <owner-chemistry^^^ccl.net> wrote:
Sent to CCL by: Peter Pinski [peter.pinski-forum=-=web.de]
Hello,

excuse me, if I am wrong. but I have tried the sort function and it
seemed that it sorts in an ALPHANUMERICAL order and not in a numerical,
i.e. 889<991 but 1021<991 !!! because 1<9.

Maybe I have just used the command in a wrong way because I usually use
Linux rather than Windows and it really is possible to use dos sort for
this job - in this case again I would like to apologise - but I don't
think the sort command is the right thing if it makes an output like this:

>sort test.txt
1021.02454
890.15454
991.1510

content of test.txt:

890.15454
1021.02454
991.1510

Sincerely,
Peter Pinski

Phil Hultin hultin- -cc.umanitoba.ca schrieb:
> Sent to CCL by: "Phil Hultin" [hultin[a]cc.umanitoba.ca]
> This is a multi-part message in MIME format.
>
> ------=_NextPart_000_0046_01C66DC4.72111EA0
> Content-Type: text/plain;
> charset="us-ascii"
> Content-Transfer-Encoding: 7bit
>
> I have been a bit amused by all the suggestions to help Richard Wood with
> his question about sorting 2x10^6 lines of text.
>
>
>
> The majority opinion has been to use some other operating system and to
> learn a new scripting language. Did nobody actually read Richard's specific
> statement that he needed something to run under windows, and that was free?
>
>
>
> I once again point out that windows still contains a perfectly functional
> command line text sorter (oddly enough, called "SORT"), and it will do
> exactly what is required using the specified operating system with no more
> learning than just reading the help file. One line of input required, with
> arguments to specify the input and output files, and which column of text to
> sort on, as well as other useful parameters.
>
>
>
> Nothing against all the suggestions people made - these are very nice ways
> to do the required task. They just don't meet the customer's specification.
>
>
>
> Dr. Philip G. Hultin
>
> Associate Professor of Chemistry,
>
> University of Manitoba
>
> Winnipeg, MB
>
> R3T 2N2
>
> hultin__cc.umanitoba.ca
>
> http://umanitoba.ca/chemistry/people/hultin
>
>
>
>
> ------=_NextPart_000_0046_01C66DC4.72111EA0
> Content-Type: text/html;
> charset="us-ascii"
> Content-Transfer-Encoding: quoted-printable
>
> > xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
> xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
> xmlns:st1=3D"urn:schemas-microsoft-com:office:smarttags" =
> xmlns=3D"http://www.w3.org/TR/REC-html40">
>
>
> > charset=3Dus-ascii">
>
> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
> name=3D"State"/>
> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
> name=3D"City"/>
> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
> name=3D"PlaceName"/>
> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
> name=3D"PlaceType"/>
> > namespaceuri=3D"urn:schemas-microsoft-com:office:smarttags"
> name=3D"place"/>
>
>
>
>
>
>
>
>

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>I have been a bit amused by all the suggestions to =
> help
> Richard Wood with his question about sorting 2x10^6 lines of =
> text.

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'> 

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>The majority opinion has been to use some other =
> operating
> system and to learn a new scripting language.  Did nobody actually =
> read Richard’s
> specific statement that he needed something to run under windows, and =
> that was
> free?

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'> 

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>I once again point out that windows still contains a
> perfectly functional command line text sorter (oddly enough, called =
> “SORT”),
> and it will do exactly what is required using the specified operating =
> system
> with no more learning than just reading the help file.  One line of =
> input
> required, with arguments to specify the input and output files, and =
> which
> column of text to sort on, as well as other useful =
> parameters.

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'> 

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>Nothing against all the suggestions people made =
> –
> these are very nice ways to do the required task.  They just =
> don’t meet
> the customer’s specification.

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'> 

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>Dr. Philip G. Hultin

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>Associate Professor of =
> Chemistry,

>
>
> u2:st=3D"on">
> w:st=3D"on">
> =
> style=3D'font-size:10.0pt;font-family:Arial'>University
> 1:PlaceType>
> size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'>
> of > w:st=3D"on">Manitoba
> ace>
> size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'>
>
>
> u2:st=3D"on">
> w:st=3D"on">> style=3D'font-size:10.0pt;font-family:
> Arial'>Winnipeg> face=3DArial>
> style=3D'font-size:10.0pt;font-family:Arial'>, > u2:st=3D"on">
> =
> w:st=3D"on">MB
>>
> size=3D2 face=3DArial>> style=3D'font-size:10.0pt;font-family:Arial'>
>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>R3T 2N2

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>> href=3D"mailto:hultin__cc.umanitoba.ca">hultin__cc.umanitoba.ca
> :p>

>
>
> style=3D'font-size:10.0pt;
> font-family:Arial'>> href=3D"http://umanitoba.ca/chemistry/people/hultin">http://umanitoba.ca/=
> chemistry/people/hultin

>
>
> style=3D'font-size:
> 12.0pt'> 

>
>

>
>
>
>
>
> ------=_NextPart_000_0046_01C66DC4.72111EA0-->
>
>
>








--
Gustavo A. Mercier, Jr. MD,PhD
Baylor University Medical Center
Radiology
American Radiology Associates
712 N. Washington, Suite 101
Dallas, TX 75246
214-826-8822
214-826-9792 fax
gamercier^^^yahoo.com 
--0-898632598-1146596113=:39457-- From owner-chemistry@ccl.net Tue May 2 23:11:01 2006 From: "Serena Povia sp422[-]hermes.cam.ac.uk" To: CCL Subject: CCL: help needed << out of hand? Message-Id: <-31674-060502201746-1284-np682dmazBtaH+HZ5HzWuw(-)server.ccl.net> X-Original-From: Serena Povia Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 3 May 2006 01:17:36 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Serena Povia [sp422*o*hermes.cam.ac.uk] Ok, the thread went slightly out of hand. The poor Rich will have an heart attack checking the email after a dreadful non-CC-working day, for how many ppl are arguing on his innocent sorting help request. We have several point of view, linux geeks (in which I'm trying to sneak in), allergic to the evilness of Win, Win users who riesumate dusty, yet useful, DOS commands, being told off by the penguin lovers. Equilibrated ppl suggested a bash simulator, which I appreciated a lot. Nevertheless the discussion seems to be spiraling down as a contrapposition of different churches. lol My opinion might biased but I suggest that we all wait for Rich's reply, before going ahead on discussing the undoubtable advantages of what we believe in (the penguin? or the Gates?) Rich, any feedback? warmest regards, Serena On Tue, 2 May 2006, Dr. N. SUKUMAR nagams**rpi.edu wrote: > Sent to CCL by: "Dr. N. SUKUMAR" [nagams^_^rpi.edu] > This discussion brings out several curious features about scientific > practice today: > > On the one hand, we have some who would rather spend hours cutting and > pasting between Word and Excel (with who knows how many mistakes in the > process) than spend the time to write 5 lines of > perl/python/DOS/bash-under-Cygwin Script to do the job once and forever. > > On the other hand, the suggestion to use a DOS command is criticized > because no one uses command line DOS anymore. Of course, that is SUCH a > good reason. Yes, I know lots of lay people (using computers for email) > who would have a heart attack at the mere thought of opening up that > little black box known as the command prompt, but here?? on CCL? Rather > spend hours with InstallShieldWizard and rebooting multiple times than > open up that little black box? > > At the same time, those who suggested perl/python scripts (all of which > run under Windows) are criticized because this is not what the "customer" > asked for. Well, if it was a paying customer, this makes sense and that > would be the end of that. But here it is a fellow scientist seeking > ADVICE, not a customer demanding a specific PRODUCT. If folks are > approaching CCL as customers trying to get products for free, there's no > reason for the rest of us to be volunteering time and expertise here. > > There are multiple ways of getting most jobs done and opinions will > always differ on the relative merits of different strategies, depending > upon our specific requirements and individual expertise and constraints. > Being exposed to multiple strategies is what enables each of us to make > an informed choice specific to our circumstances. > > Dr. N. Sukumar > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute> > > >