From chemistry-request@ccl.net Mon May 3 00:00:53 2004 Received: from mail.pas.rochester.edu (mail1.pas.rochester.edu [128.151.144.211]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4350qkh025286 for ; Mon, 3 May 2004 00:00:52 -0500 Received: from localhost.localdomain (localhost.localdomain [127.0.0.1]) by mail.pas.rochester.edu (Postfix) with ESMTP id E718A1E1599 for ; Mon, 3 May 2004 01:02:24 -0400 (EDT) Received: from mail.pas.rochester.edu (localhost.localdomain [127.0.0.1]) by localhost.localdomain (VaMailArmor-2.0.1.13) id 31303-27A3B642; Mon, 03 May 2004 01:02:24 -0400 Received: from nowshell.pas.rochester.edu (nowshell.pas.rochester.edu [128.151.144.230]) by mail.pas.rochester.edu (Postfix) with ESMTP id CECA11E1598 for ; Mon, 3 May 2004 01:02:24 -0400 (EDT) Date: Mon, 3 May 2004 01:02:31 -0400 (EDT) From: Ravindra VenKatramani To: Subject: Rigid body simulations in charmm In-Reply-To: <20040501191758.91420.qmail=at=web21208.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.13; VAE: 6.25.0.3; VDF: 6.25.0.44; host: mail1.pas.rochester.edu) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Group, I have a small (18 atom) dipeptide in DMSO solution. I would like to perform a simulation keeping both the peptide and the solvent rigid. My first thought is to define the dipeptide structure only thorugh bonds (no angles or dihederals) and use SHAKE to keep the peptide fixed. Doing so i`m running into SHAKE convergence problems during the heating and equilibration stage. Am i missing something in this simple minded approach? Is there an alternate way to perform rigid body simulations? Regards Ravi From chemistry-request@ccl.net Mon May 3 08:55:59 2004 Received: from unq.edu.ar ([200.49.110.238]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43Dtpkh016942 for ; Mon, 3 May 2004 08:55:57 -0500 Received: from unq142.unq.edu.ar by unq.edu.ar (Cipher TLSv1:RC4-MD5:128) (MDaemon.PRO.v6.8.5.R) with ESMTP id 46-md50000000226.tmp for ; Mon, 03 May 2004 10:44:31 -0300 Message-Id: <6.0.3.0.0.20040503103141.0351a780*at*correo.unq.edu.ar> X-Sender: mlema*at*correo.unq.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Mon, 03 May 2004 10:31:42 -0300 To: chemistry*at*ccl.net From: =?iso-8859-1?Q?Mart=EDn?= Lema Subject: point mutants modeling Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-Spam-Processed: unq.edu.ar, Mon, 03 May 2004 10:44:31 -0300 (not processed: spam filter disabled) X-Return-Path: mlema*at*unq.edu.ar X-MDaemon-Deliver-To: chemistry*at*ccl.net X-Spam-Status: No, hits=1.9 required=7.5 tests=DNS_FROM_RFCI_DSN,NO_RDNS2, RM_ft_Iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i43Dtxkh016946 Dear CCLs: Please suppose I have the experimental structure of a protein, and I want to use it for obtaining in silico the putative structure of single point mutants (performing a residue substitution, a sidechain replacement). By analyzing different articles I have found either people using someone else 4s algorithms, or that someone introducing his algorithm by using limited examples, but I cannot find an article that reviews many available methods for this purpose, neither one that performs a comparative assessment (again, for this specific purpose) or any article of this kind that could let me know to what extent this general problem (obtaining in silico the structure of simple point mutants from a WT structure) is solved. Would you be so kind referring me articles of this kind? Thanking in advance, Martin P.S.: An assessment like the one stated above should be based in the comparison of experimentally obtained mutant protein structures with the modeled ones, and on that basis, now I am even wondering if the combined uncertainties derived from the current resolution scale in PDB structures for two structures (the experimental mutant and the modeled mutant that cannot be better than the WT from which it derives) is actually of lower scale than the structural changes introduced by most point mutations? (in that case that assessment is imposible) ml Martmn Lema Universidad Nacional de Quilmes Roque Saenz Peqa 180 B1876BXD - Bernal Argentina From chemistry-request@ccl.net Mon May 3 08:35:44 2004 Received: from mail-gw.uniroma2.it (smtp.uniroma2.it [160.80.6.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43DZekh016301 for ; Mon, 3 May 2004 08:35:42 -0500 Received: (from root@localhost) by mail-gw.uniroma2.it (8.12.9/8.11.1) id i43CotUQ028599 for ; Mon, 3 May 2004 14:50:55 +0200 Received: from dkfz.de (afrodite.eln.uniroma2.it [160.80.80.254]) by mail-gw.uniroma2.it (8.12.9/8.11.3) with ESMTP id i43CojTN028034 for ; Mon, 3 May 2004 14:50:45 +0200 Message-ID: <40964B04.2060109-.at.-dkfz.de> Date: Mon, 03 May 2004 15:37:08 +0200 From: Thomas Niehaus User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry-.at.-ccl.net Subject: Code to compute STO one-center 2e integrals Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-AntiVirus: scanned for viruses! X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'ers, is anybody of you aware of a free Fortran/C/Maple/Matlab/.... code to compute one-center two-electron integrals from Slater-type orbitals? Many thanks in advance! Thomas Niehaus German Cancer Research Center Heidelberg From chemistry-request@ccl.net Mon May 3 03:18:17 2004 Received: from mr4.cc.ic.ac.uk (mr4.cc.ic.ac.uk [155.198.5.114]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i438IFkh007225 for ; Mon, 3 May 2004 03:18:16 -0500 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr4.cc.ic.ac.uk with esmtp (Exim 3.36 #1) id 1BKYg8-0004sN-04 for CHEMISTRY.-at-.ccl.net; Mon, 03 May 2004 09:19:56 +0100 Received: from dyn2152-170.vpn.ic.ac.uk ([194.82.152.170] helo=[194.82.152.151]) by chcmga.ch.ic.ac.uk with esmtp (Exim 3.36 #1) id 1BKYhs-00BNXf-00 for CHEMISTRY.-at-.ccl.net; Mon, 03 May 2004 09:21:44 +0100 Mime-Version: 1.0 X-Sender: rzepa.-at-.argon.ch.ic.ac.uk Message-Id: In-Reply-To: <20040501191758.91420.qmail.-at-.web21208.mail.yahoo.com> References: <20040501191758.91420.qmail.-at-.web21208.mail.yahoo.com> Date: Mon, 3 May 2004 09:19:19 +0100 To: CHEMISTRY.-at-.ccl.net From: "Rzepa, Henry" Subject: CCL: Examples of DG maxima where no PE maximum exists? Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net In the temporary absence of a working search of the CCL archives, does anyone know of any examples of the following scenario? The potential energy surface of a dissociative reaction may often rise to the asymptotic maximum of infinite separation of the two components. These two components will show a large increase in the entropy, and hence any free energy increase for this process will be substantially less than the potential energy increase. Depending on how the entropy evolves along the reaction path, its possible to imagine that unlike the potential energy, the free energy reaction path may show a clear maximum (transition state) unmatched by one in the potential energy. Does anyone know of any "classic" examples of such entropy induced transition states? (its the sort of concept that eg a Scifinder search is difficult to formulate for) -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) From chemistry-request@ccl.net Mon May 3 07:04:15 2004 Received: from mehl.gfz-potsdam.de (mehl.gfz-potsdam.de [139.17.1.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43C4Dkh013653 for ; Mon, 3 May 2004 07:04:14 -0500 Received: from nfw1.gfz-potsdam.de (virscan [139.17.1.10]) by mehl.gfz-potsdam.de (8.12.10/8.12.10) with SMTP id i43C5nse010872 for ; Mon, 3 May 2004 14:05:53 +0200 (MET DST) Received: from exp17.gfz-potsdam.de ([139.17.140.117]) by nfw1; Mon, 03 May 2004 14:05:46 +0200 (CEST) Mime-Version: 1.0 (Apple Message framework v613) To: Computational Chemistry List Message-Id: <36070816-9CFA-11D8-9036-000A95BA19DA.-at-.gfz-potsdam.de> Content-Type: multipart/alternative; boundary=Apple-Mail-1-52048258 From: Matthias Gottschalk Subject: CCL:PBC with G03 Date: Mon, 3 May 2004 14:05:46 +0200 X-Mailer: Apple Mail (2.613) X-Spam-Status: No, hits=3.5 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_1, MK_BAD_HTML_04,MY_BAD_DOT,MY_HTML_OBFU,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-1-52048258 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Dear CCL, I try to do the following thermochemistry calculation of Si with G03: %chk=si.chk %mem=2048MB %nproc=2 # freq pbepbe/3-21g/auto pressure=0.9869233 Silicium 0 1 Si 0.00000000 0.00000000 0.00000000 Si 1.35775250 1.35775250 1.35775250 Si 0.00000000 2.71550500 2.71550500 Si 4.07325750 1.35775250 4.07325750 Si 2.71550500 0.00000000 2.71550500 Si 1.35775250 4.07325750 4.07325750 Si 2.71550500 2.71550500 0.00000000 Si 4.07325750 4.07325750 1.35775250 Tv 5.43119460 0.00000000 0.00000000 Tv 0.00000000 5.43119460 0.00000000 Tv 0.00000000 0.00000000 5.43119460 The runs terminates with: . . . Generalized Minimum Residual for N= 512 ITol= 0 MaxL= 512 KMP= 512 Iter Natral Err Est Error Estimate ISDGMR: 0 .5273182E-07 .5273182E-07 ISDGMR: 1 .5143458E-07 .5143458E-07 ISDGMR: 2 .4578164E-07 .4578164E-07 ISDGMR: 3 .2232057E-07 .2232057E-07 ISDGMR: 4 .4649069E-08 .4649069E-08 ISDGMR: 5 .1595532E-08 .1595532E-08 ISDGMR: 6 .1289499E-08 .1289499E-08 ISDGMR: 7 .1043629E-08 .1043629E-08 ISDGMR: 8 .7334301E-09 .7334301E-09 IErr= 0 Err= 7.33E-10 NSaved= 6 NIter= 8 NITot= 15. PS= 112.000000000000 PSN= 112.000000000000 RNE= 112.000000000000 Err= 0.00E+00 SCF Done: E(RPBE-PBE) = -2302.99130262 A.U. after 6 cycles Convg = .8121E-08 -V/T = 2.0048 S**2 = .0000 Range of M.O.s used for correlation: 1 104 NBasis= 104 NAE= 56 NBE= 56 NFC= 0 NFV= 0 NROrb= 104 NOA= 56 NOB= 56 NVA= 48 NVB= 48 PBC SCF information not saved. Error termination via Lnk1e in /Applications/g03/l801.exe at Mon May 3 13:36:40 2004. Job cpu time: 0 days 3 hours 54 minutes 1.0 seconds. File lengths (MBytes): RWF= 1928 Int= 0 D2E= 0 Chk= 58 Scr= 1 What went wrong? What did I wrong? Thanks, Matthias -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-1-52048258 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Dear CCL, I try to do the following thermochemistry calculation of Si with G03: Courier%chk=si.chk %mem=2048MB %nproc=2 # freq pbepbe/3-21g/auto pressure=0.9869233 Silicium 0 1 Si 0.00000000 0.00000000 0.00000000 Si 1.35775250 1.35775250 1.35775250 Si 0.00000000 2.71550500 2.71550500 Si 4.07325750 1.35775250 4.07325750 Si 2.71550500 0.00000000 2.71550500 Si 1.35775250 4.07325750 4.07325750 Si 2.71550500 2.71550500 0.00000000 Si 4.07325750 4.07325750 1.35775250 Tv 5.43119460 0.00000000 0.00000000 Tv 0.00000000 5.43119460 0.00000000 Tv 0.00000000 0.00000000 5.43119460 The runs terminates with: . . . Courier Generalized Minimum Residual for N= 512 ITol= 0 MaxL= 512 KMP= 512 Iter Natral Err Est Error Estimate ISDGMR: 0 .5273182E-07 .5273182E-07 ISDGMR: 1 .5143458E-07 .5143458E-07 ISDGMR: 2 .4578164E-07 .4578164E-07 ISDGMR: 3 .2232057E-07 .2232057E-07 ISDGMR: 4 .4649069E-08 .4649069E-08 ISDGMR: 5 .1595532E-08 .1595532E-08 ISDGMR: 6 .1289499E-08 .1289499E-08 ISDGMR: 7 .1043629E-08 .1043629E-08 ISDGMR: 8 .7334301E-09 .7334301E-09 IErr= 0 Err= 7.33E-10 NSaved= 6 NIter= 8 NITot= 15. PS= 112.000000000000 PSN= 112.000000000000 RNE= 112.000000000000 Err= 0.00E+00 SCF Done: E(RPBE-PBE) = -2302.99130262 A.U. after 6 cycles Convg = .8121E-08 -V/T = 2.0048 S**2 = .0000 Range of M.O.s used for correlation: 1 104 NBasis= 104 NAE= 56 NBE= 56 NFC= 0 NFV= 0 NROrb= 104 NOA= 56 NOB= 56 NVA= 48 NVB= 48 PBC SCF information not saved. Error termination via Lnk1e in /Applications/g03/l801.exe at Mon May 3 13:36:40 2004. Job cpu time: 0 days 3 hours 54 minutes 1.0 seconds. File lengths (MBytes): RWF= 1928 Int= 0 D2E= 0 Chk= 58 Scr= 1 Courier What went wrong? What did I wrong? Thanks, Matthias Courier -- PD Dr. Matthias Gottschalk GeoForschungsZentrum Projektbereich 4.1 Telegrafenberg 14473 Potsdam Germany tel/fax +49 (0) 331 288-1418/1402 --Apple-Mail-1-52048258-- From chemistry-request@ccl.net Mon May 3 10:45:37 2004 Received: from mail.kemi.dtu.dk (mail.kemi.dtu.dk [130.225.67.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43FjZkh021425 for ; Mon, 3 May 2004 10:45:36 -0500 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.6/8.11.6) with ESMTP id i43FlCw18723; Mon, 3 May 2004 17:47:12 +0200 Mime-Version: 1.0 X-Sender: pon)at(mail.kemi.dtu.dk Message-Id: In-Reply-To: References: <20040501191758.91420.qmail)at(web21208.mail.yahoo.com> Date: Mon, 3 May 2004 17:45:43 +0200 To: "Rzepa, Henry" From: Per-Ola Norrby Subject: Re: CCL:Examples of DG maxima where no PE maximum exists? Cc: CHEMISTRY)at(ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net >In the temporary absence of a working search of the CCL archives, >does anyone know of any examples of the following scenario? > >The potential energy surface of a dissociative reaction may often >rise to the asymptotic maximum of infinite separation of the two >components. These two components will show a large increase in >the entropy, and hence any free energy increase for this process will be >substantially less than the potential energy increase. Depending >on how the entropy evolves along the reaction path, its possible to >imagine that >unlike the potential energy, the free energy reaction path may >show a clear maximum (transition state) unmatched by one in the >potential energy. > >Does anyone know of any "classic" examples of such >entropy induced transition states? >(its the sort of concept that eg a Scifinder search is difficult >to formulate for) We published one a few years ago, for the Cu-catalyzed cyclopropanation: Chem. Eur. J. 2002, 8, 177-184. This is a dangerous one to study: there are several publications based on ethylene, where you DO have a TS, but with any substituent, there is no TS on the PES, only on the free energy surface (and it's quite different from the one on the PES). Best regards, Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon)at(kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@ccl.net Mon May 3 11:30:21 2004 Received: from mx5.net.nih.gov (mx5.net.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43GUKkh022532 for ; Mon, 3 May 2004 11:30:21 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i43GW3qB025436 for ; Mon, 3 May 2004 12:32:03 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i43GW3d3025363; Mon, 3 May 2004 12:32:03 -0400 Date: Mon, 3 May 2004 12:28:14 -0400 From: Rick Venable To: Ravindra VenKatramani cc: chemistry..at..ccl.net Subject: Re: CCL:Rigid body simulations in charmm In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable..at..nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Mon, 3 May 2004, Ravindra VenKatramani wrote: > I have a small (18 atom) dipeptide in DMSO solution. I > would like to perform a simulation keeping both the peptide and the > solvent rigid. > My first thought is to define the dipeptide structure only > thorugh bonds (no angles or dihederals) and use SHAKE to keep the > peptide fixed. Doing so i`m running into SHAKE convergence problems > during the heating and equilibration stage. Am i missing something in > this simple minded approach? Is there an alternate way to perform > rigid body simulations? If there are freely rotatable single bonds, constraining the bond lengths isn't sufficient. Also, as the potential is a balance of all the terms, turning off the ANGLE and DIHEDRAL terms can lead to distortion of the structure away from accepted geometries. A couple alternatives for the mini-peptide are: [1] CONS HARM BESTFIT (cons.doc); the peptide can essentially be RMS restrained vs. its initial geometry, w/o restricting translation or whole molecule rotation. The atom selection used will determine how much of the molecule is restrained. [2] CONS IC (cons.doc, intcor.doc); the bonds, angles, and dihedrals can be restrained vs. their initial geometry. An edited IC table may be desirable, to allow free rotation of e.g. methyl groups while restraining the backbone and main sidechain configurations. The RESIDUE description for DMSO should probably have dummy C-C and O-O bonds with zero force constant, so that SHAKE can be used to make the molecule rigid, as is done for the TIP3 model via the dummy H-H bond. Finally, be sure to minimize using the exact same setup (SHAKE, boundary conditions, non-bond options) as will be used for the simulation. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable..at..nih.gov ALT email: rvenable..at..speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Mon May 3 09:48:34 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43EmXkh019524 for ; Mon, 3 May 2004 09:48:34 -0500 Received: by leitl.org (Postfix, from userid 500) id 0312B3A80E3; Mon, 3 May 2004 16:50:12 +0200 (CEST) Date: Mon, 3 May 2004 16:50:12 +0200 From: Eugen Leitl To: "Rzepa, Henry" , chemistry_at_ccl.net Subject: Re: CCL:Examples of DG maxima where no PE maximum exists? Message-ID: <20040503145012.GE25728_at_leitl.org> References: <20040501191758.91420.qmail_at_web21208.mail.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i X-Spam-Status: No, hits=0.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Mon, May 03, 2004 at 09:19:19AM +0100, Rzepa, Henry wrote: > In the temporary absence of a working search of the CCL archives, > does anyone know of any examples of the following scenario? Google might be not completely up to date, but using site restriction might work: http://www.google.com/search?q=site%3Accl.net&hl=en&num=100&btnG=Google+Search -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net From chemistry-request@ccl.net Mon May 3 14:48:48 2004 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43Jmjkh028991 for ; Mon, 3 May 2004 14:48:45 -0500 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i43JoOr5011009; Mon, 3 May 2004 15:50:24 -0400 (EDT) Date: Mon, 3 May 2004 15:50:22 -0400 Subject: Re: CCL:Rigid body simulations in charmm Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v553) Cc: To: Ravindra VenKatramani From: Richard Gillilan In-Reply-To: Message-Id: <1D3622FF-9D3B-11D8-BAEC-000393D59F68*at*cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=3.1 required=7.5 tests=MY_CHARPARENS,NO_EXPERIENCE, NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Monday, May 3, 2004, at 01:02 AM, Ravindra VenKatramani wrote: > > Dear Group, > > I have a small (18 atom) dipeptide in DMSO solution. I would > like to perform a simulation keeping both the peptide and the solvent > rigid. > My first thought is to define the dipeptide structure only > thorugh > bonds (no angles or dihederals) and use SHAKE to keep the peptide > fixed. > Doing so i`m running into SHAKE convergence problems during the heating > and equilibration stage. Am i missing something in this simple minded > approach? Is there an alternate way to perform rigid body simulations? > > Regards > Ravi Yes, there are several alternative ways which are more efficient and numerically stable. I remember reading somewhere that SHAKE is problematic when trying to define true rigid bodies. There is a program called MBO(N)D available from Accelrys (I don't know if there is a free version or not, but the code is related to CHARMM I think ... I have no relationship to this program or the company and have no experience running it). I believe the program was described in J. Comput. Chem. a few years ago: Chun HM et. al. J. Comput. Chem. 2000, 21, 159 There have also been many articles on direct rigid body integration (most recently by Miller et. al. JCP 2002, 116, 8649 ... see also Dullweber, JCP 1997, 107, 5840). Don't know if their codes are available anywhere yet. The older program DPOLY can do this kind of simulation. XPLOR also implements it, though the algorithm they use is rather old now. You may find some other codes that are specialized for liquid simulation ... I would love to know about them. Richard Gillilan MacCHESS, Cornell From chemistry-request@ccl.net Mon May 3 13:54:42 2004 Received: from maya.uab.es (maya.uab.es [158.109.0.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i43Isfkh027377 for ; Mon, 3 May 2004 13:54:42 -0500 Received: from CONVERSION-DAEMON.maya.uab.es by maya.uab.es (PMDF V6.2-X20 #30859) id <0HX500301J5MOK*at*maya.uab.es> for chemistry*at*ccl.net; Mon, 03 May 2004 20:53:47 +0200 (MEST) Received: from klingon.uab.es (klingon.uab.es [158.109.14.5]) by maya.uab.es (PMDF V6.2-X20 #30859) with ESMTP id <0HX500J4GJ5M4M*at*maya.uab.es> for chemistry*at*ccl.net; Mon, 03 May 2004 20:53:46 +0200 (MEST) Received: from localhost ([127.0.0.1] helo=klingon.uab.es ident=olivier) by klingon.uab.es with esmtp (Exim 4.30) id 1BKiJh-0006u6-A5 for chemistry*at*ccl.net; Mon, 03 May 2004 20:37:25 +0200 Date: Mon, 03 May 2004 20:37:25 +0200 From: olivier maresca Subject: Dielectric constant To: chemistry*at*ccl.net Message-id: <20040503183426.M28035*at*klingon.uab.es> MIME-version: 1.0 X-Mailer: Open WebMail 1.81 20021127 Content-type: text/plain; charset=iso-8859-1 X-OriginatingIP: 158.109.14.83 (olivier) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, CClers: Does anyone know how to compute the dielectric constant of a mixture of two liquids ? Thanks Olivier -- Open WebMail Project (http://openwebmail.org) Debian Project (http://www.debian.org)