From chemistry-request@server.ccl.net Wed Jun 20 20:55:29 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5L0tS507625 for ; Wed, 20 Jun 2001 20:55:28 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id IAA11781 for ; Thu, 21 Jun 2001 08:54:24 +0800 (CDT) Message-Id: <200106210054.IAA11781@mail.shcnc.ac.cn> Date: Thu, 21 Jun 2001 8:49:35 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear members: today,I asked the question about AMBER sander module. I received some answers . you are true. My input file goes wrong.thanks for your answers. thanksRoss and Chris and Cui !!!!!! my another question about non-AMBER parameters of the organic molecule also received some answers, the summarization as follows: msg-msg Do you have this program ???? Thank You msg-msg +-----------------------------------------------------+ Dr. Jaime Rubio Modelization of Biological Systems and Drug Design Research Group Dep. Quimica Fisica Facultat de Quimica Universitat de Barcelona C/ Marti i Franques 1 08080 Barcelona, Spain e-mail: j.rubio@qf.ub.es WWW http://www.qf.ub.es/c2/area4b3/jaime/jaime.html Tel. : (34)-93 402 12 22 Fax : (34)-93 402 1231 +-----------------------------------------------------+ another answer suggest me to reference the amber.pdf .(in Appendice 3) thanks for your reply! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Wed Jun 20 23:55:10 2001 Received: from hotmail.com ([216.33.236.139]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5L3tA509273 for ; Wed, 20 Jun 2001 23:55:10 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 20 Jun 2001 20:55:05 -0700 Received: from 200.183.61.138 by lw7fd.law7.hotmail.msn.com with HTTP; Thu, 21 Jun 2001 03:55:05 GMT X-Originating-IP: [200.183.61.138] From: "tek kno3" To: Arturas.Ziemys@vaidila.vdu.lt Cc: chemistry@ccl.net Subject: Re: CCL:Genetic Algorithm routine ? Date: Thu, 21 Jun 2001 00:55:05 -0300 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 21 Jun 2001 03:55:05.0401 (UTC) FILETIME=[F4BA6290:01C0FA05] >It is about Genetic Algorithm (GA) implemented in AutoDock. There >are "population", "max evaluations", "elitism" ,etc. > >Does "max evaluations" determinates the max energy evaluations needed >to produce a population? Could anyone explain briefly and the essence >of routine GA? Hi, you should take a look at the code/manual but usualy "max evaluations" are the maximum number o generations, i.e., GA optimization steps (each step should consist of (number of individuals in "population") energy evaluations). GA work throught selection of the fittest. In general, an initial population, i.e. a group of individuals (which genes correspond to the paramethers one wishes to optimize) is evaluated accordingly to your error function (e.g. energy difference, etc), then the fittest (e.g. lowest energy difference, etc) individuals are reproduced to the next generation accordingly to some genetics rules (breeding, mutation, etc). This evolution process continues till convergence or "max evaluations/generations". For a more complete review check: Rev.Comp.Chem. 10 (1997) - Richard Judson, Genetic Algorithms and Their Use in Chemistry, pp. 1-73. or just do a web search... hope it helps, cheers, Guilherme Menegon IQUSP - Brazil _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Thu Jun 21 00:59:48 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5L4xm510365 for ; Thu, 21 Jun 2001 00:59:48 -0400 Received: from eten (eten.ee.sc.edu [129.252.22.151]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id N224QFLM; Thu, 21 Jun 2001 00:54:29 -0400 Message-ID: <001a01c0fa0f$05309fa0$9716fc81@ee.sc.edu> From: "Hernan P Figueroa" To: Subject: CCL:Crystal message error Date: Thu, 21 Jun 2001 00:59:57 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0017_01C0F9ED.7DCB1340" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0017_01C0F9ED.7DCB1340 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello I am a graduate student, when I run crystal, with the Palladium input = set, I receive the next message in the .out file: =20 .... .... 1 PD 30 11.6721 22.0571 1 PD -5 1 1 1 PD 5-1-1 1 PD = -5 1 3 1 PD 5-1-3 1 PD -5 3 1 1 PD = 5-3-1 1 PD -3-3 3 1 PD 3 3-3 1 PD = -3-1-1 1 PD 3 1 1 1 PD -3-1 5 1 PD = 3 1-5 1 PD -3 3-3 1 PD 3-3 3 1 PD = -3 3 3 1 PD 3-3-3 1 PD -3 5-1 1 PD = 3-5 1 1 PD -1-3-1 1 PD 1 3 1 1 PD = -1-3 5 1 PD 1 3-5 1 PD -1-1-3 1 PD = 1 1 3 1 PD -1-1 5 1 PD 1 1-5 1 PD = -1 5-3 1 PD 1-5 3 1 PD -1 5-1 1 PD = 1-5 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT SYMM CPU = 0.055 ERROR **** EXCPOL **** DIMENSION OF SS12 INSUFFICIENT - INCREASE INZLS = 108864 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ERR CPU = 0.058 I have increased the neighbor number, trying with several combinations = of number, but this error message appears again. Also I tried to get the energy information of the copper crystal, but = the value never converge. I think I have to increase tha accuracy or the = number of interactions. Crystal did 50 interactions and didn't give me a = consist value. Could someone tell me which setting I have to change? Thanks in advance for your help Hernan Figueroa ------=_NextPart_000_0017_01C0F9ED.7DCB1340 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello
I am a graduate student, when I run=20 crystal, with the Palladium input set, I receive the next = message in=20 the .out file:
 
....
....
   1 PD  = 30   =20 11.6721    22.0571   1 PD  -5 1 = 1   1=20 PD   5-1-1   1 PD  -5 1=20 3
           &n= bsp;           &nb= sp;           =20 1 PD   5-1-3   1 PD  -5 3 1   1=20 PD  =20 5-3-1
          &nbs= p;            = ;            = =20 1 PD  -3-3 3   1 PD   3 3-3   1 = PD =20 -3-1-1
          &nb= sp;           &nbs= p;            = ;=20 1 PD   3 1 1   1 PD  -3-1 5   1=20 PD   3=20 1-5
           =             &= nbsp;           =20 1 PD  -3 3-3   1 PD   3-3 3   1 = PD  -3 3=20 3
           &n= bsp;           &nb= sp;           =20 1 PD   3-3-3   1 PD  -3 5-1   1=20 PD   3-5=20 1
           &n= bsp;           &nb= sp;           =20 1 PD  -1-3-1   1 PD   1 3 1   1 = PD  -1-3=20 5
           &n= bsp;           &nb= sp;           =20 1 PD   1 3-5   1 PD  -1-1-3   1=20 PD   1 1=20 3
           &n= bsp;           &nb= sp;           =20 1 PD  -1-1 5   1 PD   1 1-5   1 = PD  -1=20 5-3
           =             &= nbsp;           =20 1 PD   1-5 3   1 PD  -1 5-1   1=20 PD   1-5 1
 
 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT = SYMM     CPU      =20 0.055
 ERROR **** EXCPOL **** DIMENSION OF SS12 INSUFFICIENT - = INCREASE=20 INZLS   =20 108864
 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT=20 ERR      = CPU      =20 0.058
 
I have increased the neighbor number, = trying=20 with several combinations of number, but this error message appears=20 again.
 
Also I tried to get the energy = information of=20 the copper crystal, but the value never converge. I think I have to = increase tha=20 accuracy or the number of interactions. Crystal did 50 interactions and = didn't=20 give me a consist value.
 
Could someone tell me which setting I = have to=20 change?
Thanks in advance for your = help
 
Hernan = Figueroa
------=_NextPart_000_0017_01C0F9ED.7DCB1340-- From chemistry-request@server.ccl.net Thu Jun 21 11:35:07 2001 Received: from arha.ciens.ula.ve ([150.185.128.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5LFYe530105 for ; Thu, 21 Jun 2001 11:34:42 -0400 Received: from leviatan (jcuervo@leviatan.ciens.ula.ve [150.185.129.254]) by arha.ciens.ula.ve (8.9.1a/8.9.1) with ESMTP id LAA08754 for ; Thu, 21 Jun 2001 11:22:52 -0400 (GMT-0400) Date: Thu, 21 Jun 2001 11:46:25 -0400 (GMT) From: Javier Eduardo Cuervo Sanchez X-Sender: jcuervo@leviatan To: chemistry@ccl.net Subject: Gamess Error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's I'm runing a geometry optimizacion of a gallium-sulfur vitreous system and i got an unexpected error, the output file: ITER EX DEM TOTAL ENERGY E CHANGE DENSITY CHANGE ORB. GRAD PRD: NODE 0 ENCOUNTERED UNEXPECTED END OF FILE READING UNIT 8 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Fri Jun 8 10:20:49 2001 STEP CPU TIME = 60.18 TOTAL CPU TIME = 1176.9 ( 19.6 MIN) TOTAL WALL CLOCK TIME= 1595.1 SECONDS, CPU UTILIZATION IS 73.78% 853439 WORDS OF DYNAMIC MEMORY USED *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 DATA SERVER STATS: TOTAL DISTRIBUTED MEMORY USED (MEMDDI)= 0 MWORDS. FIRST DATA SERVER'S MAXIMUM MEMORY= 0 WORDS, CPU= .0 SECONDS. IF YOU WANT A CORE FILE, SET COREFL=.TRUE. IN $SYSTEM. The input file: $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT ICHARG=-2 MULT=1 NPRINT=-2 MAXIT=200 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $STATPT NSTEP=100 $END $SYSTEM MWORDS=10 TIMLIM=10000 $END $DATA Dimero. Cn 1 GA S 1 2.1425594 S 1 2.2583216 2 115.5332525 S 1 2.2577724 2 105.5917212 3 116.7657288 0 S 1 2.2391334 2 119.7790783 3 -126.5964541 0 GA 2 2.1402716 1 119.6449823 3 60.6357398 0 S 6 2.2614185 2 117.8157253 1 -62.8231618 0 S 6 2.2396026 2 116.2882690 1 65.1354206 0 S 6 2.2600081 2 107.0546642 1 -177.9179311 0 C 3 1.8337944 1 102.1815363 2 36.8053117 0 C 4 1.8327629 1 101.8894557 2 -176.8906050 0 C 5 1.8339937 1 103.6787861 2 74.2001842 0 C 7 1.8341035 6 103.6846520 2 78.9257691 0 C 8 1.8337560 6 101.9274436 2 172.6327696 0 C 9 1.8326124 6 101.7600803 2 48.1343417 0 H 10 1.0866301 3 111.3380717 1 61.0982383 0 H 10 1.0865811 3 109.1405672 1 -179.4598792 0 H 10 1.0862750 3 111.1899201 1 -59.9104487 0 H 11 1.0864157 4 111.2766851 1 56.4547070 0 H 11 1.0868650 4 109.3572775 1 176.1155327 0 H 11 1.0864388 4 111.4723310 1 -64.2152599 0 H 12 1.0862933 5 111.2885925 1 56.5472945 0 H 12 1.0863290 5 108.8206082 1 175.7502320 0 H 12 1.0865404 5 111.5210973 1 -64.8244408 0 H 13 1.0862743 7 111.2408685 6 53.5463059 0 H 13 1.0863690 7 108.9236892 6 172.7685494 0 H 13 1.0864654 7 111.4899190 6 -67.6841774 0 H 14 1.0863240 8 111.4209710 6 54.5432000 0 H 14 1.0866920 8 109.2179813 6 174.2771431 0 H 14 1.0864271 8 111.3440647 6 -66.1722440 0 H 15 1.0869077 9 111.3898796 6 69.1670317 0 H 15 1.0867755 9 109.3797939 6 -171.3597521 0 H 15 1.0861165 9 111.0850120 6 -51.5358280 0 $END Thanks in advance for any help Javier Cuervo From chemistry-request@server.ccl.net Thu Jun 21 09:02:26 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5LD2Q527659 for ; Thu, 21 Jun 2001 09:02:26 -0400 Received: from hpserv.imim.es (hpserv.imim.es [193.144.6.104]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id JAA25038 for ; Thu, 21 Jun 2001 09:02:20 -0400 (EDT) Received: from imim.es (i21.imim.es [193.144.6.190]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id NJRCG2ZH; Thu, 21 Jun 2001 15:02:11 +0200 Sender: hteran@ccl.net Message-ID: <3B31EFC6.399EBB18@imim.es> Date: Thu, 21 Jun 2001 14:59:50 +0200 From: "Hugo G. de Teran" X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: ADAM CC: CHEMISTRY@ccl.net Subject: Re: CCL:hyperchem database References: <001a01c0f9ac$0750c980$ccaa7180@dynamic.rpi.edu> Content-Type: multipart/alternative; boundary="------------590563051CB8207183418982" --------------590563051CB8207183418982 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Here you can find diverse sets of molecules in diverse formats. I hope it can help you http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html ADAM wrote: > Hello all My name is Adam Stradling and I am a undergraduate > researcher at Rensellear Polytechnic Institute (RPI) in Troy > NY. I was curious if anyone could direct me to a database of > hyperchem files. I need a large set of relatively common molecules. > Otherwise I will have to build them myself which could be pretty time > consuming. > thanks > Adam -- Hugo G. de Teran Castañon G. R. Informatica Biomedica Institut Municipal de Investigacio Medica - IMIM C/ Dr Aiguader, 80,E-08003/ Barcelona (SPAIN) e-mail: hteran@imim.es Ph: +34 93 221 10 09 ext 2340 Fax: Fax: +34 93 221 3237 http://www1.imim.es/modeling --------------590563051CB8207183418982 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Here you can find diverse sets of molecules in diverse formats. I hope it can help you
http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html
ADAM wrote:
Hello all        My name is Adam Stradling and I am a undergraduate researcher at Rensellear Polytechnic Institute (RPI) in Troy NY.         I was curious if anyone could direct me to a database of hyperchem files. I need a large set of relatively common molecules. Otherwise I will have to build them myself which could be pretty time consuming.                                                            thanks                                                                Adam
-- 
Hugo G. de Teran Castañon
G. R. Informatica Biomedica
Institut Municipal de Investigacio Medica - IMIM
C/ Dr Aiguader, 80,E-08003/ Barcelona (SPAIN)
e-mail: hteran@imim.es
Ph: +34 93 221 10 09 ext 2340
Fax: Fax: +34 93 221 3237
                    
                    http://www1.imim.es/modeling
  --------------590563051CB8207183418982-- From chemistry-request@server.ccl.net Thu Jun 21 12:49:16 2001 Received: from Princeton.EDU ([128.112.129.120]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5LGnG531981 for ; Thu, 21 Jun 2001 12:49:16 -0400 Received: from smtpserver1.Princeton.EDU (smtpserver1.Princeton.EDU [128.112.129.65]) by Princeton.EDU (8.9.3/8.9.3) with ESMTP id MAA10515 for ; Thu, 21 Jun 2001 12:49:15 -0400 (EDT) Received: from phoenix.Princeton.EDU (phoenix.Princeton.EDU [128.112.128.42]) by smtpserver1.Princeton.EDU (8.9.3/8.9.3) with ESMTP id MAA26017 for ; Thu, 21 Jun 2001 12:49:15 -0400 (EDT) Received: from localhost (jarzecki@localhost) by phoenix.Princeton.EDU (8.9.1/8.9.1) with ESMTP id MAA28660 for ; Thu, 21 Jun 2001 12:49:14 -0400 (EDT) Date: Thu, 21 Jun 2001 12:49:14 -0400 (EDT) From: "Andrzej A. Jarzecki" To: chemistry@ccl.net Subject: ARGUS help Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to track down the computational package ARGUS developend by Mark Thompson. Does someone know the active site to download this program? Could someone help? Sincerely, Andrzej Jarzecki jarzecki@princeton.edu From chemistry-request@server.ccl.net Thu Jun 21 14:39:03 2001 Received: from mail2.organik.uni-erlangen.de ([131.188.127.212]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5LId2501486 for ; Thu, 21 Jun 2001 14:39:02 -0400 Received: from ccc.chemie.uni-erlangen.de (wtewael [131.188.127.223]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id UAA23113; Thu, 21 Jun 2001 20:39:00 +0200 (MET DST) Sender: Wolf-Dietrich.Ihlenfeldt@ccc.chemie.uni-erlangen.de Message-ID: <3B323F43.EA8A6BAA@ccc.chemie.uni-erlangen.de> Date: Thu, 21 Jun 2001 20:39:00 +0200 From: Wolf-Dietrich Ihlenfeldt Organization: Computer Chemistry Center X-Mailer: Mozilla 4.7 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "Hugo G. de Teran" , CHEMISTRY@ccl.net, ADAM Subject: Re: CCL:hyperchem database References: <001a01c0f9ac$0750c980$ccaa7180@dynamic.rpi.edu> <3B31EFC6.399EBB18@imim.es> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Hugo G. de Teran" wrote: > > Here you can find diverse sets of molecules in diverse formats. I hope > it can help you > http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html > > ADAM wrote: Well, close, but not really a hit. There are NO Hyperchem files there. However, our WWW NCI DB V2 database interface, which contains a superset of the data on the site you cited, does have Hyperchem export capabilities. Please visit http://www2.ccc.uni-erlangen.de/ncidb2 or http://cactus.nci.nih.gov/ncidb2 look up interesting structures, and export in Hyperchem format as many structures as you need. Regards > > > Hello all My name is Adam Stradling and I am a undergraduate > > researcher at Rensellear Polytechnic Institute (RPI) in Troy > > NY. I was curious if anyone could direct me to a database of > > hyperchem files. I need a large set of relatively common molecules. > > Otherwise I will have to build them myself which could be pretty > > time > > consuming. > > thanks > > Adam > > > -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ From chemistry-request@server.ccl.net Thu Jun 21 15:59:08 2001 Received: from popserver.healthtech.com ([140.239.39.130]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5LJx8502558 for ; Thu, 21 Jun 2001 15:59:08 -0400 Received: by popserver.healthtech.com from localhost (router,SLMail V4.3); Thu, 21 Jun 2001 15:58:59 -0400 for Received: from CHRISW [140.239.39.168] by popserver.healthtech.com [140.239.39.130] (SLmail 4.3.0.3454) with SMTP id 8A746F298A8D4C8B95C55C56FB7CC0F3 for ; Thu, 21 Jun 2001 15:58:55 -0400 Message-Id: <4.1.20010621155521.00afd2f0@140.239.39.130> X-Sender: eoregan@140.239.39.130 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 21 Jun 2001 15:59:06 -0400 To: chemistry@ccl.net From: "Edel O'Regan" Subject: Molecular Diversity and Organic Synthesis meeting Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_26290716==_.ALT" X-SLUIDL: A1063B4F-315E4843-81679EF5-D455DBD6 --=====================_26290716==_.ALT Content-Type: text/plain; charset="us-ascii" Cambridge Healthtech Institute will host a conference on; Exploiting Molecular Diversity and High-Throughput Organic Synthesis Feb. 11-15, 2002 San Diego. Anyone interested in sending a proposal, to be considered for a speaking slot, should forward a title and short summary to the email address below. For further details please go to the following web sites: http://www.healthtech.com/2002/mld/index.htm http://www.healthtech.com/2002/hto/index.htm Thank you. Edel. Edel O'Regan Ph.D. Conference Producer Cambridge Healthtech Institute FAX: 617-630-1325 Phone: 617-630-1323 email: eoregan@healthtech.com --=====================_26290716==_.ALT Content-Type: text/html; charset="us-ascii"
Cambridge Healthtech Institute will host a conference on;

Exploiting Molecular Diversity and High-Throughput Organic Synthesis

                Feb. 11-15, 2002 San Diego.

Anyone interested in sending a proposal, to be considered for a speaking slot, should forward a title and short summary to the email address below.

For further details please go to the following web sites:
http://www.healthtech.com/2002/mld/index.htm
http://www.healthtech.com/2002/hto/index.htm

Thank you.

Edel.



Edel O'Regan Ph.D.
Conference Producer
Cambridge Healthtech Institute
FAX: 617-630-1325
Phone: 617-630-1323
email: eoregan@healthtech.com --=====================_26290716==_.ALT-- From chemistry-request@server.ccl.net Wed Jun 20 00:30:33 2001 Received: from web4902.mail.yahoo.com ([216.115.106.27]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5K4UX508817 for ; Wed, 20 Jun 2001 00:30:33 -0400 Message-ID: <20010620043033.10121.qmail@web4902.mail.yahoo.com> Received: from [66.81.18.86] by web4902.mail.yahoo.com; Tue, 19 Jun 2001 21:30:32 PDT Date: Tue, 19 Jun 2001 21:30:32 -0700 (PDT) From: Sengen Sun Subject: phase/orbitals To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I feel that our human’s minds are totally lost in our own human tricks. What are the human tricks? SCF, HF, LCAO, DFT, etc. are the human tricks. These tricks are very valuable to relieve the natural headache of our human beings due to the multibody system problem. Our human beings feel a little bit better when computational data are close to what we see experimentally. However, we have been well hypnotized when we see the close agreement between computations and experiments. We have to wake up, forget those human tricks, and talk about the reality according to the fundamental laws of physics. Suppose we have a singlet four electron system. The first pair of electrons occupies a 3-dimensional space unit – a single MO. The second pair has to occupy a different space unit - the second single MO due to the spin repulsion and the Coulombic repulsion. Although overlapped each other, these two 3-dimensional spaces fundamentally distinguish each other according to the fundamental laws of physics. They have nothing to do with those human tricks. The indistinguishability between electrons can not suppress the distinguishability of these two spaces. How to separate these two spaces experimentally is a technical secret I would never release :). Otherwise, the physical chemists in 800 years later would have nothing to do :). For the last several decades, an intensive effort has been made mathematically in order to get approximate pictures of the single MOs. To get the pictures of single MOs experimentally could be million times more difficult than mathematically. Unfortunately, after we got the MO information mathematically, we don’t know what is the staff we got :)! This PHASE/ORBITALS issue can be simplified to whether the atomic orbitals of neutral hydrogen atom can be experimentally measured. You can not change your philosophy when you move from a simple isolated system to a complicated multibody system. The difference I believe between the neutral hydrogen and a multibody system is that the unoccupied orbitals in the latter have no physical meaning due to electron correlation, etc. But I would say that the unoccupied MOs exist physically as partitioned spaces according to the laws. I would also agree if you say otherwise on the unoccupied MOs. I would see nothing wrong if single MOs are said to be a physical concept because their physical meaning as 3-dimensional spaces for electrons to reside is clear to me. The single MOs or AOs are not lawless or spiritual fugitives. They fully comply with all the natural laws. Their shapes and dimensions are completely defined once a system is given. Therefore, I am incapable of saying that the atomic orbitals of H are beyond experimental measurement. That depends, and is a technical issue. Our minds can be kept clear and logical by following the fundamental laws of physics. DFT is highly valuable to our human beings. But in my mind, I can not see the electrons simply as a pile of mud. If we think the micro world as a pile of mud, we would eventually have nothing to do but just pray for GOD. I read quite a few publications, and they say that MOs have no physical existence or physical meanings. I would see this as a general conceptual confusion. This confusion immerged in the 90s largely due to the success of the wonderful DFT. This PHASE/ORBITALS discussion is a good opportunity to address this issue, and therefore highly valuable. Cheers again! __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Thu Jun 21 14:10:06 2001 Received: from web11907.mail.yahoo.com ([216.136.172.191]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5LIA6500861 for ; Thu, 21 Jun 2001 14:10:06 -0400 Message-ID: <20010621181005.77923.qmail@web11907.mail.yahoo.com> Received: from [150.161.5.90] by web11907.mail.yahoo.com; Thu, 21 Jun 2001 11:10:05 PDT Date: Thu, 21 Jun 2001 11:10:05 -0700 (PDT) From: Sidney Ramos Subject: Problems with Dalton1.0.1 in the RedHat7.1 !?!?! To: dalton-users@kjemi.uio.no Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL and Dalton users, I did install the new RH7.1 in the Pentium III Xeon and that have the kernel 2.4.2 with 2Gb RAM(1Gb Swap) and 20GB scratch. I did compile the Dalton 1.0.1 with the G77 without problems. All is better when I did run the calculus "test" !!! However, if I choice a molecule bigger than this, for example, a RHF calculus of NMR parameters at phenol with 6-31G* (252 basis functions), the calculus "Stop in the TWOINT section" and it writed: /progs/dalton/dalton: line 169: 4187 Limit of Size was Exceeding (core dumped) ./dalton.x >DALTON.OUT In this moment the file AOTWOINT have 2059 kb !!! I hear about problems of Linux with files bigger than 2.0Gb, this is true? if true, Do you know if this problem was fix in some Linux version ??? This is a problem of Linux or Dalton ??? What Can I do? Thanks for any advice! Best regards! Sidney Ramos Depart. of Fundamental Chemistry (DQF) UFPE - Brazil __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Thu Jun 21 13:24:28 2001 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5LHOS532557 for ; Thu, 21 Jun 2001 13:24:28 -0400 Message-ID: <20010621172421.11337.qmail@web12806.mail.yahoo.com> Received: from [63.214.191.66] by web12806.mail.yahoo.com; Thu, 21 Jun 2001 10:24:21 PDT Date: Thu, 21 Jun 2001 10:24:21 -0700 (PDT) From: Ces Bertino Subject: molecular dynamics trajectory files request To: chemistry@ccl.net Cc: cesbertino@yahoo.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I would really like to get a hold of the results of a long dynamic (1 nanosec or higher) simulation (the dynamic data) of the beginning of a protein folding simulation (hopefully solvated with explicit water molecules). Are you aware of any institution/individual which may be willing to provide the raw atom trajectory data? Thanks for your help. Regards, Ces Bertino cesbertino@yahoo.com __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Thu Jun 21 23:45:08 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5M3j7508290 for ; Thu, 21 Jun 2001 23:45:07 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.4.7) with ESMTP id 70291 for CHEMISTRY@ccl.net; Thu, 21 Jun 2001 22:43:13 -0500 Sender: yubo@ccl.net Message-ID: <3B32BEA9.50E71AF7@mail.chem.tamu.edu> Date: Fri, 22 Jun 2001 03:42:33 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Compiling G98 on RH Linux 7.1-P4 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f5M3j8508291 Hi, We've got a dual P4Xeon-1.7G workstation to do QM calculations. Redhat linux 7.1 was installed. We have source code of G98. We ordered a copy of PGI Fortran compiler several days ago. Are there some tips for compiling G98 on the combination of Linux and P4? Any experience is preferred. Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================