From chemistry-request@server.ccl.net Wed Mar 5 21:50:08 2003 Received: from mail.shcnc.ac.cn ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h262o6a20639 for ; Wed, 5 Mar 2003 21:50:07 -0500 Received: from DATA4 ([202.127.19.226]) by mail.shcnc.ac.cn (8.12.1/8.12.1) with SMTP id h26IoK9B011344 for ; Thu, 6 Mar 2003 10:50:20 -0800 (PST) Message-ID: <000f01c2e38b$113572f0$e2137fca@simm.ac.cn> Reply-To: "Mingyue Zheng" From: "Mingyue Zheng" To: Subject: Can Autodock3.0 reckon iron in? Date: Thu, 6 Mar 2003 10:49:53 +0800 Organization: SIMM MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Disposition-Notification-To: "Mingyue Zheng" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h262o8a20642 Could anyone tell me if Autodock3.0 can reckon iron in ? The receptor active site concerned includes an iron ,one of putative ways to inhibit the enzyme is that inhibitors may replace a residue ligand to the iron,which gives a complete loss of iron and hence the loss of enzyme activity. Thus I think the interaction between iron and inhibitors can not be ignored. If can not,which program may do this kind of docking? Thanks in advance. Regards. UTF-8 ********************************************** Mingyue Zheng Drug Design & Discovery Center SIMM,China Acadmy of Science 294 Tai Yuan Road, Shanghai,200031 P.R.China Tel:021-64311833-507 E-Mail:myzheng@mail.shcnc.ac.cn ********************************************** From chemistry-request@server.ccl.net Thu Mar 6 06:31:29 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26BVPa10815 for ; Thu, 6 Mar 2003 06:31:26 -0500 Received: from mail.ustc.edu.cn (webmail.ustc.edu.cn [202.38.64.16]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with SMTP id TAA02063 for ; Thu, 6 Mar 2003 19:25:13 +0800 From: bllin@mail.ustc.edu.cn Received: from 202.38.82.238 (SquirrelMail authenticated user bllin) by webmail.ustc.edu.cn with HTTP; Thu, 6 Mar 2003 19:29:11 +0800 (CST) Message-ID: <63146.202.38.82.238.1046950151.squirrel@webmail.ustc.edu.cn> Date: Thu, 6 Mar 2003 19:29:11 +0800 (CST) Subject: Convergence problem in the single-point calculations of Gaussian 98 To: X-Priority: 3 Importance: Normal X-MSMail-Priority: Normal X-Mailer: SquirrelMail (version 1.2.0 [cvs]) MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear CCLers, Could anyone here tell me how to achieve the single-point calculation if the SCF convergence fails?The calculated sturctures were obtained from optmizations with a lower basis set than that of the single-point calculation.I have tried to do some calculations with the method of lowering the convergence criteria and then restarting the SCF procedure > from the checkpoint file,where the keywords I used are "guess=read", "geom=allcheck" , and "scf=restart".Some of them have been accomplished at last,but there are still others remaining not converged if the criteria is lifted.Is there any other method that can solve this problem?Thanks a lot! Best wishes! ******************************************* Bolin Lin Department of Chemistry University of Science & Technology of China Hefei, Anhui 230026P. R. China E-mail: bllin@mail.ustc.edu.cn ******************************************* From chemistry-request@server.ccl.net Thu Mar 6 02:37:21 2003 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h267bLa24785 for ; Thu, 6 Mar 2003 02:37:21 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 6A9E0954EF2; Thu, 6 Mar 2003 08:37:20 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 6A63E954EEF; Thu, 6 Mar 2003 08:37:19 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 6 Mar 03 08:37:19 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 6 Mar 03 08:37:16 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Silva Lopez; Carlos" Date: Thu, 6 Mar 2003 08:37:03 +0100 Subject: CCL:NBO Analysis Reply-To: spanget@ruc.dk Cc: Chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: X-Spam-Status: No, hits=-3.2 required=5.0 tests=QUOTED_EMAIL_TEXT version=2.50 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.50 (1.173-2003-02-20-exp) Dear Carlos: > I have done a NBO analysis of a transition structure were a sigma > bond is being broken. The problem arises when check the orbital > structure, there is still a pi bond where the sigma bond is already > broken. Could it mean there is a certain aromaticity in that TS and > pi electrons are still creating a "current" despite of the big bond > distances. Is there any other point of view (with chemistry sense, > not mathematical formulation of anything non graspable)? Thanks You apply the NBO procedure on a "non-classical" chemical species, namely a transition state with a half-broken bond. The procedure tries to find a description of the electronic structure in terms of localized bonds and lone pairs, corresponding to a single classical Lewis formula, but this is obviously problematic for a species like the one you are investigating. The NBO procedure comes up with a compromize, and you should be careful not to overrate the chemical significance of the results of the analysis. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Mar 6 10:02:05 2003 Received: from web.concord.org ([4.19.234.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26F24a16690 for ; Thu, 6 Mar 2003 10:02:05 -0500 Received: from fc.concord.org (fc.concord.org [4.19.234.60]) by web.concord.org (8.12.5/8.12.5) with ESMTP id h26F20Vw010942 for ; Thu, 6 Mar 2003 10:02:04 -0500 Received: from dhcp221.concord.org (4.19.234.221) by fc.concord.org (FirstClass Mail Server v7.1) with ESMTP (Sender: qxie@concord.org) transient id 20; Thu, 06 Mar 2003 10:02:00 -0500 Message-Id: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> X-Sender: qxie@secure.concord.org X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 06 Mar 2003 09:20:27 -0500 To: CHEMISTRY@ccl.net From: Charles Xie Subject: Energy conservation of molecular dynamics in the presence of electrostatic forces Cc: bob@concord.org Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCLers, I have a general question about totoal energy conservation of classical molecular dynamics (MD) in the presence of electrostatic forces. Total energy is perfectly conserved when we do a typical MD with only the wan der Waals (Lennard-Jones) potentials, using a time step of one femtosecond (e.g. for the Argon gas as a classical example). Problems, however, arise when molecules are charged. Because electrostatic forces are much more long-ranged (1/r dependence) and typically stronger, the magnitude of electrostatic forces on atoms can be several hundred (or even thousand) times greater than that of van der Waals forces. As a result, the time step has to be accordingly reduced for two or three orders of magnitude, in order for the total energy to conserve. This means a time step of 0.001-0.01 femtosecond has to be applied. (EXPLAIN: Most standard algorithms, such as the Verlet method, the Gear predictor-corrector method and the Runge-Cutta method, depend on using the term a*dt^2 to compute the solution stepwisely, where a is the acceleration, dt is the time step. If this term is too large, the numerical error will rapidly propogate, and the solution will diverge. Compared with pure Lennard-Jones simulations, adding the electrostatic forces increase accelerations. Therefore, dt must be decreased in order to keep a*dt^2 down.) I can see only two ways to solve this problem, both of which turn out to be impractical, as you will see later. One is to accept the reality, use a smaller time step. But, reducing the time step to 0.001 femtosecond will slow down the simulation 1000 times (in comparison to pure Lennard-Jones simulations). You will probably never see any emerging behavior of the model because losing your temper. The other way around is to use smaller charges, as most molecular mechanics force fields do. For example, instead of using 1 for a free radical's charge, one can use 0.01 (and self-explain that this is an effective-field approximation). While this would maintain energy conservation, you might not see the emerging behaviors due to charges either --- because the electrostatic forces are so weaker than they ought to be, they might not be able to produce results that only strong interactions can exhibit, such as self-organization. Energy conservation is generally not an concern for most classic molecular dynamics simulations that assume a heat bath (for controlling the temperature to a desired value, thus remove the numerical errors resulted from large a*dt^2). However, getting the energetics right is of paramount importance to modeling exoergicity/endoergicity of chemical reactions. Unfortunately, I am not aware of anyone mentioning this before. All the molecular simulation books I have (Allen and Tildesley, Leach, Rapaport and so on) do not even mention it at all. My prior experience with CHARMm v27, if I was doing it right, is that it doesn't seem to do energy conservation, even though the NVE protocol is literally specified. I would greatly appreciate any advice and opinion. Thank you, Charles Xie International Center The Concord Consortium www.concord.org From chemistry-request@server.ccl.net Thu Mar 6 04:41:10 2003 Received: from artemis.rus.uni-stuttgart.de ([129.69.1.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h269fAa07805 for ; Thu, 6 Mar 2003 04:41:10 -0500 Received: from stephanpc (vpn-v-010.campus.uni-stuttgart.de [129.69.196.10]) by artemis.rus.uni-stuttgart.de with SMTP id KAA23699; Thu, 6 Mar 2003 10:41:00 +0100 (MET) env-from (Stephan.Tatzel@po.uni-stuttgart.de) Message-ID: <008a01c2e3c4$924f2230$0f02a8c0@stephanpc> From: "Stephan Tatzel" To: "Mingyue Zheng" Cc: "CCL-List" References: <000f01c2e38b$113572f0$e2137fca@simm.ac.cn> Subject: Re: CCL:Can Autodock3.0 reckon iron in? Date: Thu, 6 Mar 2003 10:41:32 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Yes, AutoDock 3 can recognise iron atoms. AutoGrid can recognise up to 7different atomtypes in the protein. You have to change the atomtype of the iron from Fe to M (AutoDock 1-letter atom type code) and then define the r and epsilon values to the appropriate values for the new atom type in the grid parameter file. When you use AutoDockTools to set up your dockings, the program will automatically detect an new atomtype in your protein when loading a protein with iron and ask you to change it to the Atomtype M and also ask for the appropriate r and epsilon values. For further information just look on the AutoDock homepage FAQ. There is a short tutorial How to treat an iron atom in docking. http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html Stephan ______________________________________ Stephan Tatzel Institute of Technical Biochemistry University of Stuttgart Allmandring 31 D-70569 Stuttgart, Germany Email: Stephan.Tatzel@po.uni-stuttgart.de ----- Original Message ----- From: "Mingyue Zheng" To: Sent: Thursday, March 06, 2003 3:49 AM Subject: CCL:Can Autodock3.0 reckon iron in? > Could anyone tell me if Autodock3.0 can reckon iron in ? > The receptor active site concerned includes an iron ,one of putative ways to inhibit the enzyme is that inhibitors may replace a residue ligand to the iron,which gives a complete loss of iron and hence the loss of enzyme activity. Thus I think the interaction between iron and inhibitors can not be ignored. > If can not,which program may do this kind of docking? > Thanks in advance. > Regards. > UTF-8 > ********************************************** > Mingyue Zheng > Drug Design & Discovery Center > SIMM,China Acadmy of Science > 294 Tai Yuan Road, Shanghai,200031 P.R.China > Tel:021-64311833-507 > E-Mail:myzheng@mail.shcnc.ac.cn > ********************************************** > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Mar 6 09:51:03 2003 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26Ep2a16442 for ; Thu, 6 Mar 2003 09:51:03 -0500 Received: from cosmologic.de (xdsl-213-168-110-56.netcologne.de [213.168.110.56]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id AAP93501 (AUTH klamt@cosmologic.de); Thu, 6 Mar 2003 15:50:57 +0100 (CET) Message-ID: <3E676049.6020407@cosmologic.de> Date: Thu, 06 Mar 2003 15:50:49 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Full description of SDF file format Content-Type: text/plain; charset=ISO-8859-15; format=flowed Content-Transfer-Encoding: 7bit Does anyone have a full description of the sdf-file format available? Thanks in advance Andreas -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Mar 6 09:29:17 2003 Received: from ans2.spri.sp.com ([198.16.9.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26ETHa15792 for ; Thu, 6 Mar 2003 09:29:17 -0500 Received: from KENMSGRH03.schp.com by sp.spcorp.com with ESMTP id JAA29577 (InterLock SMTP Gateway 5.0 for ); Thu, 6 Mar 2003 09:29:34 -0500 (EST) Received: from kenmsgbham05.us.schp.com (unverified) by KENMSGRH03.schp.com (Content Technologies SMTPRS 4.3.6) with ESMTP id ; Thu, 6 Mar 2003 09:29:14 -0500 Received: by kenmsgbham05.schp.com with Internet Mail Service (5.5.2653.19) id ; Thu, 6 Mar 2003 09:29:13 -0500 Message-ID: <51E9450E2DA1D4118DB400508BF9AC3406C2F611@kenmsg32.schp.com> From: "Madison, Vincent" To: "'chemistry@ccl.net'" Cc: "'jkl@ccl.net'" Subject: James Kaminski Date: Thu, 6 Mar 2003 09:29:08 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed; boundary="----_=_NextPart_000_01C2E3EC.BF3D7C60" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01C2E3EC.BF3D7C60 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C2E3EC.BF3D7C60" ------_=_NextPart_001_01C2E3EC.BF3D7C60 Content-Type: text/plain Please post a notice on the CCL. Dr. James J. Kaminski died on March 1st at the age of 55. Jim was prominent in the computational chemistry community and co-authored more than 80 scientific papers and 25 U.S. patents. He was a leader in the CADD group at Schering-Plough where he worked for 25 years. Jim was respected for his expertise and sage counsel. He was beloved for his optimism, sense of humor and trademark laugh. See the URL below for an obituary from the Newark Star Ledger. http://www.nj.com/obituaries/ledger/index.ssf?/base/news-23/104677027843610. xml (I've also attached a photo for possible posting) Thank You, Vincent Madison Distinguished Fellow Drug Design Group Schering-Plough Research Institute (908) 740-3979 <> ********************************************************************* This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. ------_=_NextPart_001_01C2E3EC.BF3D7C60 Content-Type: text/html Content-Transfer-Encoding: quoted-printable James Kaminski

        Please post a notice on the CCL.

        Dr. James J. Kaminski died on March 1st at the age of 55.  Jim was pr= ominent in the computational chemistry community and co-authored more than = 80 scientific papers and 25 U.S. patents.  He was a leader in the CADD= group at Schering-Plough where he worked for 25 years.  Jim was respe= cted for his expertise and sage counsel.  He was beloved for his optim= ism, sense of humor and trademark laugh.  See the URL below for an obi= tuary from the Newark Star Ledger.

  http://www.nj.com/obituaries/= ledger/index.ssf?/base/news-23/104677027843610.xml
      = ; =20
(I've also attached a photo for possible = posting)

Thank You,

Vincent Madison
Distinguished Fellow
Drug Design Group
Schering-Plough Research Institute
(908) 740-3979


<<Jim_Kaminski.jp= g>>



*********************************************************************
This message and any attachments are solely for the intended recipient. If = you are not the intended recipient, disclosure, copying, use or distributio= n of the information included in this message is prohibited -- Please immed= iately and permanently delete.
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5KXL8d7QeRfp9oP1L6qv1X7f+7Of95yr398EWhPV6p4fs16YQl3bvXt8v9rJMDzQlzy4/B07eFK+ 2BIYF5v9X9GXm5CejJz4btTietaDJCrR7n5m6v6H1q75dfVffv1PQHvmbl+s03nkWJXZh9U8R8dR vX7tiOuU9Aw2+CHPLiOvChp18e1P45Lddvx7vx8XR+pU8qEVGx2PXHdJV6nwi+8f0yXo/Fs/V5/Y /wD/2Q== ------_=_NextPart_000_01C2E3EC.BF3D7C60-- From chemistry-request@server.ccl.net Thu Mar 6 11:36:53 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26Gaqa19472 for ; Thu, 6 Mar 2003 11:36:52 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id QAA62767; Thu, 6 Mar 2003 16:36:45 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18qyIO-00025T-00; Thu, 06 Mar 2003 16:32:36 +0000 Date: Thu, 6 Mar 2003 16:32:36 +0000 (GMT) From: Szilveszter Juhos To: "Dr. Andreas Klamt" cc: "chemistry@ccl.net" Subject: Re: CCL:Full description of SDF file format In-Reply-To: <3E676049.6020407@cosmologic.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Does anyone have a full description of the sdf-file format available? http://www.mdl.com/downloads/literature/ctfile.pdf np Szilva From chemistry-request@server.ccl.net Thu Mar 6 12:20:27 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26HKRa21557 for ; Thu, 6 Mar 2003 12:20:27 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h26HKQP24775 for ; Thu, 6 Mar 2003 09:20:26 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 10506; Thu, 06 Mar 2003 09:12:21 -0800 (PST) Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h26HKOv22722; Thu, 6 Mar 2003 09:20:24 -0800 (PST) Received: from quine.scripps.edu (dhcp-252-206 [137.131.252.206]) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id JAA130449; Thu, 6 Mar 2003 09:20:24 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Thu, 6 Mar 2003 09:20:21 -0800 Date: Thu, 6 Mar 2003 09:20:21 -0800 From: "David A. Case" To: Charles Xie Cc: chemistry@ccl.net Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostatic forces Message-ID: <20030306172021.GA440@scripps.edu> References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> User-Agent: Mutt/1.4i On Thu, Mar 06, 2003, Charles Xie wrote: > > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. I think something is wrong here: the electrostatic forces for reasonable chemical models are not larger than vdW forces, and all of the significant contributions to the force come from nearby atoms. Is it possible you are confusing energy with force? > My prior experience with CHARMm v27, if I was doing it right, is that it > doesn't > seem to do energy conservation, even though the NVE protocol is literally > specified. This program should be conserving energy with a 1 fs time step. Certainly the nearly parallel CHARMM program does, as do other popular simulation codes. Of course, this could depend critically on parameters you would specify, particularly the cutoffs. ..hope this helps...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Thu Mar 6 12:47:16 2003 Received: from web.concord.org ([4.19.234.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26HlGa22356 for ; Thu, 6 Mar 2003 12:47:16 -0500 Received: from fc.concord.org (fc.concord.org [4.19.234.60]) by web.concord.org (8.12.5/8.12.5) with ESMTP id h26HlGVw016052; Thu, 6 Mar 2003 12:47:16 -0500 Received: from dhcp221.concord.org (4.19.234.221) by fc.concord.org (FirstClass Mail Server v7.1) with ESMTP (Sender: qxie@concord.org) transient id 34; Thu, 06 Mar 2003 12:47:15 -0500 Message-Id: <5.1.1.6.2.20030306122652.00afbb28@secure.concord.org> X-Sender: qxie@secure.concord.org X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Thu, 06 Mar 2003 12:47:05 -0500 To: "David A. Case" From: Charles Xie Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostati Cc: CHEMISTRY@ccl.net In-Reply-To: References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Thank you for your answer. At 12:20 PM 3/6/2003 -0500, you wrote: >On Thu, Mar 06, 2003, Charles Xie wrote: > >> > >> Problems, however, arise when molecules are charged. Because > >> electrostatic forces are much more long-ranged (1/r dependence) and > >> typically stronger, the magnitude of electrostatic forces on atoms can > >> be several hundred (or even thousand) times greater than that of van > >> der Waals forces. > > >I think something is wrong here: the electrostatic forces for reasonable >chemical models are not larger than vdW forces, and all of the significant >contributions to the force come from nearby atoms. Is it possible you are >confusing energy with force? If the electrostatic energy is greater, shouldn't the forces be greater? I understand that there are cancellations because of positive and negative charges scattered around. But overall, the forces should (??) be larger. For example, suppose we play with a Lennard-Jones system. If epsilon is increased, we will definitely observe an increasing of melting point. The implication of this is that the interatomic forces are greater, so the atoms cooperatively resist the raising of temperature. I am currently dealing with gaseous phase reactions. What I did is very simple. I started from a Lennard-Jones gas, added charges to them. And I found it hard to get total energy conservation. > >> My prior experience with CHARMm v27, if I was doing it right, is that > >it > >> doesn't > >> seem to do energy conservation, even though the NVE protocol is > >literally > >> specified. > > >This program should be conserving energy with a 1 fs time step. Certainly >the nearly parallel CHARMM program does, as do other popular simulation >codes. >Of course, this could depend critically on parameters you would specify, >particularly the cutoffs. Is there any rule in determining the charges of atoms in CHARMm's force fields? They look to a novice like me randomly chosen. >..hope this helps...dac > >-- Definitely. Thanks a lot. >================================================================== >David A. Case | e-mail: case@scripps.edu >Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 >The Scripps Research Institute | phone: +1-858-784-9768 >10550 N. Torrey Pines Rd. | home page: >La Jolla CA 92037 USA | http://www.scripps.edu/case >================================================================== From chemistry-request@server.ccl.net Thu Mar 6 11:41:48 2003 Received: from evans.univer.kharkov.ua ([80.92.225.132]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26Geca19608 for ; Thu, 6 Mar 2003 11:40:41 -0500 Received: from spin.univer.kharkov.ua (spin.univer.kharkov.ua [192.168.213.252]) by evans.univer.kharkov.ua (8.12.6/8.12.5) with SMTP id h26GeAfS029511; Thu, 6 Mar 2003 18:40:15 +0200 Received: by spin.univer.kharkov.ua with Microsoft Mail id <01C2E40F.3D79F3C0@spin.univer.kharkov.ua>; Thu, 6 Mar 2003 18:36:02 +0200 Message-ID: <01C2E40F.3D79F3C0@spin.univer.kharkov.ua> From: "sergey i. kotelevskii" To: "'p smith'" , "'CCL community'" Subject: RE: infra-red stretching frequencies Date: Thu, 6 Mar 2003 18:36:01 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h26Gfma19629 ---------- From: p smith Sent: Friday, February 28, 2003 3:10 AM To: chemistry@ccl.net Subject: CCL:infra-red stretching frequencies Hello, It depends. That is, the cheapest/reliable method depends on the system under study. For qualitative purposes on large stable systems, you may use AM1 or PM3 frequencies scaling them heavily above ~ 1500-2000 cm(-1). However, you couldn't expect reliability e.g. from Hydrogen-bonded complexes in low-frequency region. As the cheapest universal tool, DFT B3LYP is recommended, with mandatory polarization functions on heavy atoms (and hydrogens for X-H stretch). Also take a look at: A.P.Scott and L. Radom, "Harmonic Vibrational Frequencies: An Evaluation of Hartree-Fock, Moller-Plesset, Quadratic Configurational Interaction, Density Functional Theory, and Semiempirical Scale Factors", J. Phys. Chem. 1996, V.100, 16502-16513. Best regards, Serghey. **************************************************************************************** Serghey I. Kotelevskii, Department of Theoretical Chemistry and Astrochemistry, Research Institute for Chemistry, Kharkiv VNKarazin National University, Svobody Square 4, UA-61077 Kharkiv, Ukraine Hi, What is the cheapest method of producing reliable IR stretching frequencies computationally i.e. which represents the best compromise between cost and accuracy. I know these calculations can be performed semi-empirically but I am not sure how accurate the results are. Cheers, Paul p.smith@student.umist.ac.uk From chemistry-request@server.ccl.net Thu Mar 6 12:49:42 2003 Received: from mail-d.bcc.ac.uk ([144.82.100.24]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26Hnga22453 for ; Thu, 6 Mar 2003 12:49:42 -0500 Received: from pop-b.ucl.ac.uk by mail-d.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 6 Mar 2003 17:49:39 +0000 Received: from pop-d.ucl.ac.uk (pop-d.ucl.ac.uk [144.82.100.34]) by pop-b.ucl.ac.uk (8.11.6+Sun/8.9.3) with ESMTP id h26HnaM09646; Thu, 6 Mar 2003 17:49:36 GMT Sender: mb@ucl.ac.uk Message-ID: <3E678762.BFE86976@ucl.ac.uk> Date: Thu, 06 Mar 2003 17:37:38 +0000 From: M Brunsteiner Organization: UCL X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Charles Xie CC: CHEMISTRY@ccl.net, bob@concord.org Subject: Re: CCL:Energy conservation of molecular dynamics in the presence ofelectrostatic forces References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner: Found to be clean dear Charles, I do not agree with what you say. Energy is usually conserved well, provided you a) account for the long range interactions properly with Ewald or any equivalent method or at least use a force-shifted or switched coulomb potential (It is well knwon that applying a cutoff to the (particularly Coulomb) forces will heat your system up. b) use a symplectic integration scheme such as any version of the Verlet algorithm (and NOT Runge Kutta or Gear, ...) If you do so and still end up with a divergent energy then there's something wrong with the program or your input, if you ask me. If you allow for chemical reactions, however, then the energy will of course not be conserved (and if so than this would be a coincidence) unless you treat the whole system on an ab-initio basis, because, for example, the chemical binding energy of a covalent bond is of course not properly included in a classical MD Hamiltonian. And you seem to talk about classical MD in your mail, don't you ? Chemical reactions are not supposed to happen in such a system. best wishes, mic Charles Xie wrote: > > Dear CCLers, > > I have a general question about totoal energy conservation of classical > molecular dynamics (MD) in the presence of electrostatic forces. > > Total energy is perfectly conserved when we do a typical MD with > only the wan der Waals (Lennard-Jones) potentials, using a time > step of one femtosecond (e.g. for the Argon gas as a classical example). > > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. As a result, the time step has to be accordingly > reduced for two or three orders of magnitude, in order for the total > energy to conserve. This means a time step of 0.001-0.01 femtosecond > has to be applied. > > (EXPLAIN: Most standard algorithms, such as the Verlet method, the Gear > predictor-corrector method and the Runge-Cutta method, depend on using > the term a*dt^2 to compute the solution stepwisely, where a is the > acceleration, > dt is the time step. If this term is too large, the numerical error will > rapidly > propogate, and the solution will diverge. Compared with pure Lennard-Jones > simulations, adding the electrostatic forces increase accelerations. > Therefore, > dt must be decreased in order to keep a*dt^2 down.) > > I can see only two ways to solve this problem, both of which turn out to be > impractical, as you will see later. > > One is to accept the reality, use a smaller time step. But, reducing the time > step to 0.001 femtosecond will slow down the simulation 1000 times (in > comparison to pure Lennard-Jones simulations). You will probably never see > any emerging behavior of the model because losing your temper. > > The other way around is to use smaller charges, as most molecular mechanics > force fields do. For example, instead of using 1 for a free radical's charge, > one can use 0.01 (and self-explain that this is an effective-field > approximation). > While this would maintain energy conservation, you might not see the > emerging behaviors due to charges either --- because the electrostatic forces > are so weaker than they ought to be, they might not be able to produce > results that only strong interactions can exhibit, such as self-organization. > > Energy conservation is generally not an concern for most classic molecular > dynamics simulations that assume a heat bath (for controlling the temperature > to a desired value, thus remove the numerical errors resulted from large > a*dt^2). > However, getting the energetics right is of paramount importance to modeling > exoergicity/endoergicity of chemical reactions. Unfortunately, I am not aware > of anyone mentioning this before. All the molecular simulation books I have > (Allen and Tildesley, Leach, Rapaport and so on) do not even mention it at all. > My prior experience with CHARMm v27, if I was doing it right, is that it > doesn't > seem to do energy conservation, even though the NVE protocol is literally > specified. > > I would greatly appreciate any advice and opinion. > > Thank you, > > Charles Xie > > International Center > The Concord Consortium > www.concord.org > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ========================================================================== "Emotions are alien to me. I'm a scientist." (Spock, "This Side of Paradise", stardate 3417.3) -------------------------------------------------------------------------- Michael Brunsteiner Centre for Theoretical and Computational Chemistry University College London mailto:m.brunsteiner@ucl.ac.uk http://www.ucl.ac.uk/~uccambr/ -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Mar 6 11:51:11 2003 Received: from novalfsmtp2.novsvcs.net ([192.208.44.111]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26GpBa19963 for ; Thu, 6 Mar 2003 11:51:11 -0500 Received: from ukrgsmtp02.cp.chbs ([147.167.242.114]) by novalfsmtp2.novsvcs.net (8.10.2/8.9.3) with ESMTP id h26Gotn16836; Thu, 6 Mar 2003 11:50:55 -0500 Received: from ukrgmsxhub10.cp.chbs (ukrgmsxhub10.cp.chbs [147.167.242.94]) by ukrgsmtp02.cp.chbs (Build 103 8.9.3/NT-8.9.3) with ESMTP id QAA02338; Thu, 06 Mar 2003 16:50:57 GMT From: graham.mullier@syngenta.com Received: by ukrgmsxhub10.cp.chbs with Internet Mail Service (5.5.2653.19) id ; Thu, 6 Mar 2003 16:50:53 -0000 Message-ID: <0B27450D68F1D511993E0001FA7ED2B3025E4B9A@ukjhmbx12.ukjh.zeneca.com> To: andreas.klamt@cosmologic.de Cc: chemistry@ccl.net Subject: RE: Full description of SDF file format Date: Thu, 6 Mar 2003 16:50:48 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-15" Andreas, it's on the MDL web site as a PDF - see http://www.mdli.com/downloads/literature/ctfile.pdf Regards, Graham Graham Mullier Chemoinformatics Team Leader, Chemistry Design Group, Syngenta, Bracknell, RG42 6EY, UK. direct line: +44 (0) 1344 414163 mailto:Graham.Mullier@syngenta.com -----Original Message----- From: Dr. Andreas Klamt [mailto:andreas.klamt@cosmologic.de] Sent: 06 March 2003 14:51 To: chemistry@ccl.net Subject: CCL:Full description of SDF file format Does anyone have a full description of the sdf-file format available? Thanks in advance Andreas -- ---------------------------------------------------------------------------- ---- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt@cosmologic.de web: www.cosmologic.de ---------------------------------------------------------------------------- ---- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ---------------------------------------------------------------------------- ---- -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Mar 6 12:13:45 2003 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26HDha20922 for ; Thu, 6 Mar 2003 12:13:43 -0500 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id SAA04395 ; Thu, 6 Mar 2003 18:12:33 +0100 (MET) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen To: CHEMISTRY@ccl.net Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostatic forces Date: Thu, 6 Mar 2003 18:11:12 +0100 User-Agent: KMail/1.4.3 References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> In-Reply-To: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Cc: Charles Xie MIME-Version: 1.0 Message-Id: <200303061811.12617.hinsen@cnrs-orleans.fr> X-MailScanner: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h26HDla20923 On Thursday 06 March 2003 15:20, you wrote: > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. As a result, the time step has to be accordingly > reduced for two or three orders of magnitude, in order for the total > energy to conserve. This means a time step of 0.001-0.01 femtosecond > has to be applied. That doesn't seem quite right. A long range does not imply a strong force, it just means that the force on any given atom depends on the positions of many others. The contributions can (and often do, in practice) cancel out. Moreover, large forces do not automatically imply fast motions, other parameters (e.g. temperature) enter as well. You don't say what kind of systems you study. In liquids and biomolecules at room termperature, a time step of 1 fs works perfectly well with electrostatic interactions. One does see improvement of energy conservation when going to 0.5 fs, but there is no need to go to time steps as small as those you quote. So either your system is very different, or there is a bug in your force calculation code. > Energy conservation is generally not an concern for most classic molecular > dynamics simulations that assume a heat bath (for controlling the > temperature to a desired value, thus remove the numerical errors resulted > from large a*dt^2). That depends on the thermostat that is used. Personally I prefer the extended systems method, precisely because there is still a conserved energy that can be used to monitor the behaviour of the simulation. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Mar 6 13:38:17 2003 Received: from web14201.mail.yahoo.com ([216.136.172.143]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h26IcGa23912 for ; Thu, 6 Mar 2003 13:38:16 -0500 Message-ID: <20030306183757.57418.qmail@web14201.mail.yahoo.com> Received: from [158.170.16.22] by web14201.mail.yahoo.com via HTTP; Thu, 06 Mar 2003 10:37:57 PST Date: Thu, 6 Mar 2003 10:37:57 -0800 (PST) From: carolina lorena Subject: database frag to LUDI To: chemistry@ccl.net In-Reply-To: <003101c2e3ff$5639f640$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-30864314-1046975877=:54664" --0-30864314-1046975877=:54664 Content-Type: text/plain; charset=us-ascii Hi all! Anybody know where I can download database fragment for use with LUDI (msi), I mean to the *.pdb/struct and *.inp files. In my insightII/LUDI version I only find fragment_all and fragment_link files, that database have around 1100 fragments. Thank a lot for any help. Carolina Mascayano --------------------------------- Do you Yahoo!? Yahoo! Tax Center - forms, calculators, tips, and more --0-30864314-1046975877=:54664 Content-Type: text/html; charset=us-ascii

Hi all!

Anybody know where I can download database fragment for use with LUDI
(msi), I mean to the *.pdb/struct and *.inp files.
In my insightII/LUDI version I only find fragment_all and fragment_link
files, that database have around 1100 fragments.

Thank a lot for any help.

Carolina Mascayano


Do you Yahoo!?
Yahoo! Tax Center - forms, calculators, tips, and more --0-30864314-1046975877=:54664-- From chemistry-request@server.ccl.net Thu Mar 6 13:11:23 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26IBNa23280 for ; Thu, 6 Mar 2003 13:11:23 -0500 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA15418; Thu, 6 Mar 2003 13:11:16 -0500 (EST) Message-ID: <3E6790DD.4040103@cornell.edu> Date: Thu, 06 Mar 2003 13:18:05 -0500 From: Richard Gillilan User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Charles Xie CC: CHEMISTRY@ccl.net, bob@concord.org Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostatic forces References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Charles: I am a bit confused by your results. The factor that most influences integration step size is how rapidly the potential changes with distance, not its magnitude. Electrostatic forces are much smoother and change more slowly than van der Waal's terms (1/r vs 1/r^10 or 1/r^14). A step size of 1fs should give you good energy conservation. You did not say what code you were using. The usual cause of energy conservation problems is the "stiff" nature of C-H and other similar bonds. Here are a few possible problems: 1. Numerically check the correctness of your derivatives in the force calculation. Symmetric finite difference is simple and usually works very well for this and can help track down problems. If you are using someone else's code, then you can skip this. 2. Are you using periodic boundary conditions? If one atom of a neutral dipole pair crosses the periodic boundary, you get a sudden discontinuity in the energy since the charges are now separated by a large distance. You need to apply periodic boundaries to neutral charge groups as a whole. A traditional way of dealing with this is by using cutoffs with a smooth ramp to zero at some large distance based on distance between centers of charge groups. Nowdays, folks use particle mesh Ewald or some other summation method to handle electrostatics. 3. Does the energy drift or does it just fluctuate a lot around an average? Methods like Gear and Runge-Cutta are not used in MD because, though they give very good short-time accuracy, they lack long term stability you get with a symplectic integration scheme like Verlet. If you come from a Physics background you may be accustomed to running much more accurate integrations with tighter error control. This is usually not appropriate for large-scale MD since the exponential divergence of trajectories from their initial conditions renders coordinate accuracy meaningless in less than a picosecond. MD is used mainly for sampling coordinates. Nonetheless, your energy should be stable and not drift with time. Running equivalent time periods with different time steps should show improvement in conservation as steps get small. Good luck. Richard Gillilan MacCHESS, Cornell > Dear CCLers, > > I have a general question about totoal energy conservation of classical > molecular dynamics (MD) in the presence of electrostatic forces. > > Total energy is perfectly conserved when we do a typical MD with > only the wan der Waals (Lennard-Jones) potentials, using a time > step of one femtosecond (e.g. for the Argon gas as a classical example). > > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. As a result, the time step has to be accordingly > reduced for two or three orders of magnitude, in order for the total > energy to conserve. This means a time step of 0.001-0.01 femtosecond > has to be applied. > > (EXPLAIN: Most standard algorithms, such as the Verlet method, the Gear > predictor-corrector method and the Runge-Cutta method, depend on using > the term a*dt^2 to compute the solution stepwisely, where a is the > acceleration, > dt is the time step. If this term is too large, the numerical error > will rapidly > propogate, and the solution will diverge. Compared with pure > Lennard-Jones > simulations, adding the electrostatic forces increase accelerations. > Therefore, > dt must be decreased in order to keep a*dt^2 down.) > > I can see only two ways to solve this problem, both of which turn out > to be > impractical, as you will see later. > > One is to accept the reality, use a smaller time step. But, reducing > the time > step to 0.001 femtosecond will slow down the simulation 1000 times (in > comparison to pure Lennard-Jones simulations). You will probably never > see > any emerging behavior of the model because losing your temper. > > The other way around is to use smaller charges, as most molecular > mechanics > force fields do. For example, instead of using 1 for a free radical's > charge, > one can use 0.01 (and self-explain that this is an effective-field > approximation). > While this would maintain energy conservation, you might not see the > emerging behaviors due to charges either --- because the electrostatic > forces > are so weaker than they ought to be, they might not be able to produce > results that only strong interactions can exhibit, such as > self-organization. > > Energy conservation is generally not an concern for most classic > molecular > dynamics simulations that assume a heat bath (for controlling the > temperature > to a desired value, thus remove the numerical errors resulted from > large a*dt^2). > However, getting the energetics right is of paramount importance to > modeling > exoergicity/endoergicity of chemical reactions. Unfortunately, I am > not aware > of anyone mentioning this before. All the molecular simulation books I > have > (Allen and Tildesley, Leach, Rapaport and so on) do not even mention > it at all. > My prior experience with CHARMm v27, if I was doing it right, is that > it doesn't > seem to do energy conservation, even though the NVE protocol is > literally specified. > > I would greatly appreciate any advice and opinion. > > > > From chemistry-request@server.ccl.net Thu Mar 6 14:23:33 2003 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26JNWa24869 for ; Thu, 6 Mar 2003 14:23:32 -0500 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id UAA09367 ; Thu, 6 Mar 2003 20:22:33 +0100 (MET) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen To: Charles Xie Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostati Date: Thu, 6 Mar 2003 20:21:11 +0100 User-Agent: KMail/1.4.3 Cc: CHEMISTRY@ccl.net References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> <5.1.1.6.2.20030306122652.00afbb28@secure.concord.org> In-Reply-To: <5.1.1.6.2.20030306122652.00afbb28@secure.concord.org> MIME-Version: 1.0 Message-Id: <200303062021.11954.hinsen@cnrs-orleans.fr> X-MailScanner: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h26JNXa24870 On Thursday 06 March 2003 18:47, Charles Xie wrote: > understand that there are cancellations because of positive and negative > charges scattered around. But overall, the forces should (??) be larger. But cancellation is the key point. In condensed matter, the charge density averaged over a region containing a few atoms is always very close to zero, as otherwise the electrostatic energy would be so large as to make the system unstable. > I am currently dealing with gaseous phase reactions. What I did is very That may be the cause of your problem, in gas phase, I would expect energies and forces to vary much more strongly over time, and charge cancellation to happen only on very large length scales. I wonder if standard MD is the best choice for that kind of system. Some adaptive step-size integrator that slows down only in case of near-collisions might be better. Or perhaps even a scheme similar to those used for hard-sphere systems, where the time step is obtained by estimating the time until the next collision. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------