CCL: help needed

 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"
 <owner-chemistry%ccl.net>
 >>> Reply-To: "CCL Subscribers" <chemistry%ccl.net>
 >>> To: "Wood, Richard L. " <rwoodphd%msn.com>
 >>> 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>
 >>>
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