From chemistry-request@server.ccl.net Mon Oct 14 13:33:11 2002 Received: from ws4-4.us4.outblaze.com ([205.158.62.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9EHXAf32323 for ; Mon, 14 Oct 2002 13:33:10 -0400 Received: (qmail 1486 invoked by uid 1001); 14 Oct 2002 17:33:00 -0000 Message-ID: <20021014173300.1485.qmail@linuxmail.org> Content-Type: text/plain; charset="iso-8859-15" Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: MIME-tools 5.41 (Entity 5.404) Received: from [129.69.166.31] by ws4-4.us4.outblaze.com with http for bimo7@linuxmail.org; Mon, 14 Oct 2002 19:33:00 +0200 From: "Bimo Ario Tejo" To: chemistry@ccl.net Cc: jkl@ccl.net Date: Mon, 14 Oct 2002 19:33:00 +0200 Subject: CCL: rapid heating during MD X-Originating-Ip: 129.69.166.31 X-Originating-Server: ws4-4.us4.outblaze.com Dear CCLers, I'd like to know exactly what is the effect of too rapid heating phase on molecular dynamics. I got enery potential (Ep) curve is increased sharply during heating phase (60 ps), but during production phase of 1 ns the energy looks very-very stable. The energy curve looks very nice, except during heating phase. Do I have to bother about heating phase if I took the last 100 ps as average structure which is very stable and equilibrated? Is it very important to get very smooth Ep curve during heating phase? FYI, even the energy increased too fast during heating phase, my simulation was not crashed. Regards, Bimo -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Mon Oct 14 14:04:12 2002 Received: from hotmail.com ([216.33.241.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9EI4Bf00387 for ; Mon, 14 Oct 2002 14:04:11 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 14 Oct 2002 11:04:12 -0700 Received: from 128.8.176.196 by lw8fd.law8.hotmail.msn.com with HTTP; Mon, 14 Oct 2002 18:04:11 GMT X-Originating-IP: [128.8.176.196] From: "Melanie Moses" To: chemistry@ccl.net Subject: dodecahedron Date: Mon, 14 Oct 2002 14:04:11 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 14 Oct 2002 18:04:12.0062 (UTC) FILETIME=[1995EBE0:01C273AC] Dear Colleagues, I am an inorganic graduate student trying to figure out a computational problem and was wondering if any of you may be able to give me some insight. I am trying to generate coordinates for a dodecahedron with Ih point symmetry that I can put into CAChe 4.1. I think I should start with a center atom and generate the 20 atoms around it; however, I am uncertain how to do this or what type of program would be needed. Any suggestions or insight would be appreciated. Thank you, > > Melanie Moses (melaniejmoses@hotmail.com) > Graduate Student of Bryan Eichhorn's > Department of Chemistry and Biochemistry > University of Maryland, College Park _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Mon Oct 14 14:15:15 2002 Received: from gatekeeper.itqb.unl.pt ([193.136.177.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9EIFEf00700 for ; Mon, 14 Oct 2002 14:15:15 -0400 Received: (qmail 5493 invoked from network); 14 Oct 2002 18:15:14 -0000 Received: from mistral.itqb.unl.pt (herrmann@193.136.176.14) by gatekeeper.itqb.unl.pt with SMTP; 14 Oct 2002 18:15:14 -0000 Received: from localhost (herrmann@localhost) by mistral.itqb.unl.pt (8.9.3/8.9.3) with ESMTP id TAA24818 for ; Mon, 14 Oct 2002 19:15:13 +0100 Date: Mon, 14 Oct 2002 19:15:13 +0100 (WEST) From: Rudolf Herrmann To: chemistry@ccl.net Subject: G98: VOCl3 problem: convergence criterion not met Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I recently tried to calculate the NMR chemical shifts of VOCl3 with Gaussian 98: ---------------------------------------------------------------------------- #B3LYP/6-31G* SP NMR VOCl3 0 1 cl cl 1 clcl2 cl 2 clcl3 1 clclcl3 o 3 ocl4 2 oclcl4 1 dih4 v 3 vcl5 2 vclcl5 1 dih5 clcl2 3.506363 clcl3 3.506243 clclcl3 59.999 ocl4 2.938735 oclcl4 53.376 dih4 -64.586 vcl5 2.118170 vclcl5 34.144 dih5 -31.640 ----------------------------------------------------------------------------- The result (even with several variations in the input) is always an error termination when trying the "incremental Fock formation" (convergence criterion not met). The structure was optimized with GAMESS. Any suggestion what I could do is wellcome - thank you! ------------------------------------------------------------------------------ 108 basis functions 288 primitive gaussians 41 alpha electrons 41 beta electrons nuclear repulsion energy 561.9817715949 Hartrees. One-electron integrals computed using PRISM. NBasis= 108 RedAO= T NBF= 108 NBsUse= 108 1.00D-04 NBFU= 108 Projected Huckel Guess. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.200 hartree. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -2359.59549049 A.U. after 65 cycles Convg = 0.5851D-03 -V/T = 1.9657 S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/g98_a7/l502.exe. Job cpu time: 0 days 0 hours 16 minutes 33.0 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 -------------------------------------------------------------------------- -- Dr. Rudolf Herrmann Instituto de Tecnologia Quimica e Biologica (ITQB) Av. da Republica, EAN, Apt. 127 P-2781-901 Oeiras e-mail: herrmann@itqb.unl.pt From chemistry-request@server.ccl.net Tue Oct 15 03:21:12 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9F7LBf26356 for ; Tue, 15 Oct 2002 03:21:11 -0400 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id JAA29033; Tue, 15 Oct 2002 09:19:43 +0200 (MET DST) Date: Tue, 15 Oct 2002 09:19:43 +0200 (MET DST) Message-Id: <200210150719.JAA29033@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: "Bimo Ario Tejo" , chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: CCL:rapid heating during MD Cc: jkl@ccl.net Hi, to my knowledge, the heating phase in MD calcs is needed to equilibrate the energy (or temperature) of the system to the given temperature. The equilibration time should not be taken too small, but this depends on the system you're considering. If you're interested in how a system behaves at a specific temperature, you should not take this equilibration time into consideration. Hope this helps ! Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Tue Oct 15 14:07:42 2002 Received: from mr1.cc.ic.ac.uk ([155.198.5.111]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9FI7ff09236 for ; Tue, 15 Oct 2002 14:07:41 -0400 Received: from sunfs1-gw.ps.ic.ac.uk ([155.198.164.2] helo=sunfs1.ps.ic.ac.uk) by mr1.cc.ic.ac.uk with esmtp (Exim 3.35 #1) id 181W6W-0001El-01 for CHEMISTRY@ccl.net; Tue, 15 Oct 2002 19:07:40 +0100 Received: from pskaram ([155.198.165.105]) by sunfs1.ps.ic.ac.uk with smtp (Exim 3.31 #1) id 181W6R-0005oM-00 for CHEMISTRY@ccl.net; Tue, 15 Oct 2002 19:07:35 +0100 From: "Panagiotis G. Karamertzanis" To: Subject: Gamess question Date: Tue, 15 Oct 2002 19:07:03 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Scanner: exiscan *181W6R-0005oM-00*RmT0RbB6LgA* http://duncanthrax.net/exiscan/ Dear all, I started using GAMESS recently. I am computing electrostatic potential to do later on fitting with distributed charges. The problem is that I do not know the units of the output of the GAMESS run. The manual does not help with this. Thanks, Panagiotis Karamertzanis CPSE Imperial College From chemistry-request@server.ccl.net Tue Oct 15 04:56:50 2002 Received: from hotmail.com ([64.4.32.227]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9F8uof28733 for ; Tue, 15 Oct 2002 04:56:50 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 15 Oct 2002 01:56:50 -0700 Received: from 211.161.196.196 by pv0fd.pav0.hotmail.msn.com with HTTP; Tue, 15 Oct 2002 08:56:50 GMT X-Originating-IP: [211.161.196.196] From: =?gb2312?B?1qMgw/fUwg==?= To: chemistry@ccl.net Subject: Some problems about DOCK4.0 Date: Tue, 15 Oct 2002 16:56:50 +0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 15 Oct 2002 08:56:50.0280 (UTC) FILETIME=[CCC56E80:01C27428] Hi !all CLL users I am a beginner in the field of drug design and encountered some problems on using DOCK4.O: 1)How to set parameters for "critical_points",or how to define a critical point in the receptor sphere?should I edit the *.sph file? and how?(This question was presented by Xavier Fradera on 18.sep.2002, but still no one reply.) 2)If the result vary remarkably when I modify the value of "random_seed", does it mean that model is not reliable? 3)There are references listed on the manual may be of help,but some early documents are hard for me to access.Is anyone here who have these documents ? Could you send an electonic copy to me?Thanks a lot in advance. Any suggestions or resources ,ect.would be very helpful and highly appreciated. ps : Hi,Xavier Fradera,have you had your problem solved?If so please give me a hand.Thank you! Best regards! yours sincerely Zheng _________________________________________________________________ 与联机的朋友进行交流，请使用 MSN Messenger: http://messenger.microsoft.com/cn