From chemistry-request@server.ccl.net Fri Jul 19 02:09:57 2002 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6J69vK01496 for ; Fri, 19 Jul 2002 02:09:57 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g6J69dS4024251 for ; Thu, 18 Jul 2002 23:09:39 -0700 Received: FROM dante51.u.washington.edu BY mailscan-out1.cac.washington.edu ; Thu Jul 18 23:09:39 2002 -0700 Received: from localhost (jzheng73@localhost) by dante51.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g6J69cFO111394 for ; Thu, 18 Jul 2002 23:09:38 -0700 Date: Thu, 18 Jul 2002 23:09:38 -0700 (PDT) From: "J. Zheng" cc: chemistry@ccl.net Subject: data structure for coding In-Reply-To: <1026831451.3d34345b155ae@web-mail2.uibk.ac.at> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi CCLers: I have a general question about data structure of program. Now I am involving a biological system which contains protein, water, ion and surface by using MD technique. What I want is to code a general FORTRAN program which can deal with single or multiple component system. For example, if the system contains protein, water, ion and surface, it is very straightforward to assign different components with different arrays, e.g. x(n),v(n),a(n) represent protein coordinate,velocity and acceleration. wx(3,n),wv(3,n),wa(3,n) represent water coor., velo. and acce. ionx(n),ionv(n),iona(n) represent ion coor., velo. and acce. ... Now, I am wonder that 1) is that data structure suitable to deal with biological systems? 2) how other softwares such as CHARMM, AMBER or GROMACS to handle such systems. I will appreciate your any suggestion. thanks. Jie ----------------------------------------------- | JIE ZHENG | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 616-6510 (o) | | Email: jzheng73@u.washington.edu | | Webpg: students.washington.edu/jzheng73 | ----------------------------------------------- From chemistry-request@server.ccl.net Fri Jul 19 07:54:55 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JBstK08737 for ; Fri, 19 Jul 2002 07:54:55 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id HAA14999; Fri, 19 Jul 2002 07:54:53 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D37FE0E.96CF49A@cornell.edu> Date: Fri, 19 Jul 2002 07:54:54 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: "J. Zheng" CC: chemistry@ccl.net Subject: Re: CCL:data structure for coding References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit JIE: In my opinion, it is far better to use C++ if you want good modern data structures. (Some may suggest using Python script for the user interface and C or C++ under ... this is also good, but one must be aware of the memory and performance limitations of Python). If you work carefully, performance with C++ can be quite good and the code will be much easier for others to maintain and improve (than FORTRAN) in the future. You can even check out VMD/NAMD or similar freely-available, open codes that will probably already do what you want ... in parallel. I'm sure you will hear many opionions on this. Richard Gillilan MacCHESS Cornell "J. Zheng" wrote: > > hi CCLers: > > I have a general question about data structure of program. Now I am > involving a biological system which contains protein, water, ion and > surface by using MD technique. What I want is to code a general FORTRAN > program which can deal with single or multiple component system. > From chemistry-request@server.ccl.net Fri Jul 19 09:51:00 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JDp0K11178 for ; Fri, 19 Jul 2002 09:51:00 -0400 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g6JDlRf04267; Fri, 19 Jul 2002 15:47:27 +0200 X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Sender: hinsen@chinon.cnrs-orleans.fr To: "J. Zheng" CC: chemistry@ccl.net Subject: Re: CCL:data structure for coding References: From: Konrad Hinsen Date: 19 Jul 2002 15:47:27 +0200 In-Reply-To: Message-ID: Lines: 29 User-Agent: Gnus/5.0808 (Gnus v5.8.8) Emacs/20.7 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii "J. Zheng" writes: > 1) is that data structure suitable to deal with biological systems? It's as good as many others. However, the difficulty of biological systems lies elsewhere. The rather complex force fields require a considerable effort to prepare energy evaluations, and rather complex data structures for energy terms. If you want to write a simulation program from scratch for dealing with biological systems, plan a lot of time for that. I also do not recommend using Fortran, which is not well equipped to handle the complex data structures. You might be better off starting with existing code that already does much of the work. I am aware of two codes that can handle biomolecules and that are OpenSource software, i.e. permit you to make your own modifications and pass them on to others: GROMACS (www.gromacs.org), written in C, and my own Molecular Modelling Toolkit (dirac.cnrs-orleans.fr/MMTK/), written in a mixture of Python and C. -- ------------------------------------------------------------------------------- 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 Fri Jul 19 16:34:28 2002 Received: from iris.services.ou.edu ([129.15.2.125]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JKYSK21342 for ; Fri, 19 Jul 2002 16:34:28 -0400 Received: from htwork (chem-bchm-86.chem.ou.edu [129.15.13.86]) by iris.services.ou.edu (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) with SMTP id <0GZI008MVJT49E@iris.services.ou.edu> for chemistry@ccl.net; Fri, 19 Jul 2002 15:34:16 -0500 (CDT) Date: Fri, 19 Jul 2002 15:34:29 -0500 From: haitao Subject: CHARMM+GAMESS To: chemistry@ccl.net Message-id: <000c01c22f63$aece0400$560d0f81@ou.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Mailer: Microsoft Outlook Express 5.50.4133.2400 Content-type: MULTIPART/ALTERNATIVE; BOUNDARY="Boundary_(ID_i7mVXFSLpHEtR0WAanPrcw)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_i7mVXFSLpHEtR0WAanPrcw) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT I tried to run a QM/MM jobs using CHARMM interfaced with GAMESS-US. In the GAMESS input I left the $DATA section empty (It is said that this section can be left empty). But I got an error telling me that "No $DATA group was found". Is the error because of the empty $DATA section or something else? Thanks for any help. --Boundary_(ID_i7mVXFSLpHEtR0WAanPrcw) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
I tried to run a QM/MM jobs using CHARMM interfaced with GAMESS-US. In the GAMESS input I left the $DATA section empty (It is said that this section can be left empty). But I got an error telling me that "No $DATA group was found". Is the error because of the empty $DATA section or something else?
Thanks for any help.
--Boundary_(ID_i7mVXFSLpHEtR0WAanPrcw)-- From chemistry-request@server.ccl.net Fri Jul 19 16:42:29 2002 Received: from mail.lsd.ornl.gov ([160.91.102.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JKgTK21520 for ; Fri, 19 Jul 2002 16:42:29 -0400 Received: from ornl.gov (mailbkup.lsd.ornl.gov [160.91.102.69]) by mail.lsd.ornl.gov (Postfix) with ESMTP id 924C414E46 for ; Fri, 19 Jul 2002 16:42:28 -0400 (EDT) Sender: nxy@mail.lsd.ornl.gov Message-ID: <3D3879B4.9502A58C@ornl.gov> Date: Fri, 19 Jul 2002 16:42:28 -0400 From: Dong Xu X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: release of PROSPECT 2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are pleased to announce the release of the first public beta version of PROSPECT 2. PROSPECT is a threading-based protein structure prediction system. Compared with PROSPECT 1, PROSPECT 2 substantially improves the accuracy, speed, flexibility, and ease of use, with a suite of new features: * Improved threading accuracy * Faster computing speed with less memory requirement * Updated template database from the PDB as of May, 2002 * A domain template library using SCOP * Template generation from a PDB file * A new energy function for threading with Psi-Blast profiles * Built-in secondary structure prediction * Statistical assessment of threading result using SVM * A Perl/Tk interface to run PROSPECT and browse the threading outputs. You can read about the improvements and see documentation of the new PROSPECT at http://compbio.ornl.gov/structure/prospect2/ . PROSPECT is free of charge to academic users. Please print the academic licensing agreement at the Web site and fax it to us. We will send you the information for download. We've also started the PROSPECT mailing list, prospect@mailhub.ornl.gov, in order to join, send an email to majordomo@mailhub.ornl.gov, with the body: subscribe prospect Or if you want to get the list in digest mode, subscribe prospect-digest Oak Ridge National Labs Protein Informatics Group From chemistry-request@server.ccl.net Fri Jul 19 07:39:59 2002 Received: from bbhm.na.pg.com ([192.44.184.159]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JBdxK08464 for ; Fri, 19 Jul 2002 07:39:59 -0400 X-ExtMailInfo: pandora.na.pg.com [155.118.176.101] Received: from pandora.na.pg.com (pandora.na.pg.com [155.118.176.101]) by bbhm.na.pg.com (8.8.8/8.11.1/v2r10) with ESMTP id g6JBdnT05184; Fri, 19 Jul 2002 07:39:49 -0400 (EDT) Received: from pg.com (morpheus.na.pg.com [143.5.24.124]) by pandora.na.pg.com (SGI-8.9.3/8.9.3) with ESMTP id HAA49491; Fri, 19 Jul 2002 07:32:53 -0400 (EDT) Sender: laidig@pg.com Message-ID: <3D37F8F5.8E56D427@pg.com> Date: Fri, 19 Jul 2002 07:33:10 -0400 From: Bill Laidig Reply-To: laidig@pg.com X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chanjcc@speck.niddk.nih.gov CC: CHEMISTRY@ccl.net Subject: Re: CCL:Sgi workstation for Quanta References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jerry, I think the big issue is the 32 bit nature of the O2. Our group bought one several years ago and because of various compatibility issues with software between our other SGI's we decided not to purchase anymore O2's. If it were me I would opt for the Fuel even if it costs more. Bill chanjcc@speck.niddk.nih.gov wrote: > Dear all, > > we are considering to buy a new SGI workstation for running Quanta 97. > Owing to the budget limit, we can only afford the starting configuration > of the Fuel visual workstation (SGI VPro V10 graphics, 32MB of graphics > memory, a 500MHz MIPS R14000A CPU with 2MB L2 cache, and 512MB memory). > An alternative is to get an O2+ (32 bit) with the best possible > configuration (MIPS@R12000A CPU with 2 MB L2 cache, 1 GB memory). My > question is, does it really worth going for the Fuel visual station (e.g. I > think a 50% gain in performance does not justify the Fuel)? I would be > grateful to have your suggestions. > > Regards, > Jerry > > ******************************************************************* > * Jerry C. C. Chan phone: 301-402-4687 * > * Laboratory of Chemical Physics fax: 301-496-0825 * > * Room 406, Building 5, NIDDK http://samson3.uni-muenster.de * > * National Institutes of Health * > * Bethesda, MD20892, USA * > ******************************************************************* > > -= 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 -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@server.ccl.net Fri Jul 19 12:13:16 2002 Received: from erouter0.it-datacntr.louisville.edu ([136.165.1.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JGDGK15166 for ; Fri, 19 Jul 2002 12:13:16 -0400 Received: from gwise.louisville.edu (gwise.louisville.edu [136.165.1.106]) by erouter0.it-datacntr.louisville.edu (Postfix) with ESMTP id 0685A41012 for ; Fri, 19 Jul 2002 12:13:15 -0400 (EDT) Received: from gwgate-MTA by gwise.louisville.edu with Novell_GroupWise; Fri, 19 Jul 2002 12:13:00 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Beta Date: Fri, 19 Jul 2002 12:12:47 -0400 From: "Daquan Gao" To: Subject: Re: CCL:cartesian to pdb Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Babel can only convert from one format to another, assiging residue names is not a simple conversion problem, it requires a search and compare strategy according to standard residue topologies. >>> eric hu 07/18/02 12:56 PM >>> Of course I tried Babel first which I thought is the standard way to do this kind of thing. However babel can not assign the correct residue name according the cartesian coordinates (with the atom types). Eric --- eric hu wrote: > Hi, I wonder if there is an easy way to change the > cartesian coordinates to pdb format. Thanks! > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.com > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com -= 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 Fri Jul 19 12:23:27 2002 Received: from erouter0.it-datacntr.louisville.edu ([136.165.1.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JGNRK15393 for ; Fri, 19 Jul 2002 12:23:27 -0400 Received: from gwise.louisville.edu (gwise.louisville.edu [136.165.1.106]) by erouter0.it-datacntr.louisville.edu (Postfix) with ESMTP id 8A4F541012 for ; Fri, 19 Jul 2002 12:23:25 -0400 (EDT) Received: from gwgate-MTA by gwise.louisville.edu with Novell_GroupWise; Fri, 19 Jul 2002 12:22:53 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Beta Date: Fri, 19 Jul 2002 12:22:38 -0400 From: "Daquan Gao" To: Cc: Subject: Re: CCL:cartesian to pdb Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Babel can only convert from one format to another, assiging residue names is not a simple conversion problem, it requires a search and compare strategy according to standard residue topologies. >>> eric hu 07/18/02 12:56 PM >>> Of course I tried Babel first which I thought is the standard way to do this kind of thing. However babel can not assign the correct residue name according the cartesian coordinates (with the atom types). Eric --- eric hu wrote: > Hi, I wonder if there is an easy way to change the > cartesian coordinates to pdb format. Thanks! > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.com > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com -= 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 Jul 18 22:10:19 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6J2AIr25970 for ; Thu, 18 Jul 2002 22:10:18 -0400 Message-ID: <20020719021018.30279.qmail@web12805.mail.yahoo.com> Received: from [203.87.150.242] by web12805.mail.yahoo.com via HTTP; Thu, 18 Jul 2002 19:10:18 PDT Date: Thu, 18 Jul 2002 19:10:18 -0700 (PDT) From: amor san juan Subject: Re: CCL:Problem with ADT To: "Stephen P. Molnar, Ph.D." , chemistry@ccl.net In-Reply-To: <5.1.1.6.2.20020718061716.00a048d0@jadeinc.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Dr. Molnar: I have the same problem. The platform I installed ADT is RedHat7 linux and everytime I run the program ADT "polygon offset extension failed" is flagged. I run the control distributed file 3ptb-ben and it generated ben.pdbq & 3ptb.pdbqs almost perfectly. Now, I'm trying to resolve usage of ADT with my samples. Anyone would please kindly give us hint. Sincerely, Amor San Juan University of the Philippines-Diliman --- "Stephen P. Molnar, Ph.D." wrote: > Clueless in Columbus - starting AutoDock Tools. > I've installed > complete1.5_i86Linux2_acad.tar.Z. When I start adt, > after sourcing > install.bash, I get the message: > > 'polygonOffset extension FAILED' > > I would assume this is a python error, as adt, seems > to work,. but my > question is what have I failed to install? > > I am running the SuSE v7.1 Linux distribution. > > Thanks in advance. > > > > -= 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 > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com From chemistry-request@server.ccl.net Fri Jul 19 12:18:06 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6JGI6K15274 for ; Fri, 19 Jul 2002 12:18:06 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA19411; Fri, 19 Jul 2002 12:18:04 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3D382E6D.A9D3B296@cornell.edu> Date: Fri, 19 Jul 2002 11:21:17 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CHARMM HELP NEEDED!!! References: <3D35C920.15FD350@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I just want to let everyone know that I have solved my own problem. What happened was that I was translating half of a 74.5848 A box of water 24.8616 A, instead of translating it 74.5848 A. Thus, this leads to bad contacts, and bad energy. I want to thank everyone that offered suggestions to me. Cheers, Richard "Dr. Richard L. Wood" wrote: > Hi all > > I have what I think is a very strange problem. > > I'm curently using a "big" version of CHARMm, one that will handle > 60,000+ atoms. > I have built a system that consists of a glycosylated peptide having 27 > amino acids and > 21 mannoses. The system is solvated with 14,375 TIP3P waters, giving a > total of 43,915 > atoms. When I try and calculate the energy of the system with all the > waters present, the > energy goes through the roof; that is to say, I get stars instead of > numbers for the energy. > However, if I change the number of waters in the lines > > READ SEQUENCE TIP3 8844 > GENERATE WAT NOANGLE NODIHE > > READ SEQUENCE TIP3 5531 > GENERATE WAT2 NOANGLE NODIHE > > to this: > > READ SEQUENCE TIP3 5700 > GENERATE WAT NOANGLE NODIHE > > CHARMm is able to read the structure in and calculate its energy. > > The other way, with 14,375 waters defined in the input file, it will > read the structure in, > but claculates the energy as *********. I don't want to go with only > 5700 waters as my peptide > won't be completely solvated. With the 14,375 waters, I have a shell > around the peptide about 18 A > thick. > > Obviously, I'm under the 60,000 atom limit, but I'm over some other > limit that I'm not aware of. > Has anyone encountered this problem before and how is it handled? > > Thank you in advance. > > Richard > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Food Science > 120 Stocking Hall > Cornell University, Ithaca, NY 14853 -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri Jul 19 20:12:32 2002 Received: from georgetown.edu ([141.161.1.110]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6K0CWB02108 for ; Fri, 19 Jul 2002 20:12:32 -0400 Received: from mailhost.georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by georgetown.edu (8.12.2/8.12.2) with ESMTP id g6K0CRe8024515 for ; Fri, 19 Jul 2002 20:12:27 -0400 (EDT) Received: from georgetown.edu (knauer.chemistry.georgetown.edu [141.161.37.20]) (user=knauerc mech=PLAIN bits=0) by mailhost.georgetown.edu (8.12.2/8.12.2) with ESMTP id g6K0CNjq020418 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 19 Jul 2002 20:12:26 -0400 (EDT) Message-ID: <3D38AB58.453C1A18@georgetown.edu> Date: Fri, 19 Jul 2002 20:14:16 -0400 From: knauerc Organization: Georgetown University X-Mailer: Mozilla 4.75 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Equilibrium constants Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does anyone know where I can find good data for the equilibrium constants, (as a function of temperature), for the reactions: H2 + Cl2 = 2HCL and H2 + Br2 = 2HBr Thank you. Connie Knauer Georgetown University knauerc@georgetown.edu From chemistry-request@server.ccl.net Fri Jul 19 21:12:23 2002 Received: from travelers.mail.cornell.edu ([132.236.56.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6K1CMB07179 for ; Fri, 19 Jul 2002 21:12:22 -0400 Received: from travelers.mail.cornell.edu (travelers.mail.cornell.edu [132.236.56.13]) by travelers.mail.cornell.edu (8.9.3/8.9.3) with SMTP id VAA00091; Fri, 19 Jul 2002 21:12:21 -0400 (EDT) Date: Fri, 19 Jul 2002 21:12:21 -0400 (EDT) From: rlw28@cornell.edu X-Sender: rlw28@travelers.mail.cornell.edu To: chemistry@ccl.net cc: rlw28@cornell.edu, rwood005@twcny.rr.com Subject: I have yet ANOTHER stupid CHARMM question... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all I have yet ANOTHER stupid CHARMM question. I'm doing a verlet simulation on a system other than a water box, namely my solvated peptide which I just fixed (finally). I'm currently in the process of heating my system from 100 to 300 K in 50 K steps. My question is this: what values should I use for IHTFRQ, the heating frequency, and TEMINC, the heating increment in degrees K? My 50 K heatings run last for 10,000 time teps; I've broken it up into 4 10 ps heatings. I was thinking something along these lines, namely that the number of steps divided by IHTFRQ times TEMINC should be equal to the change in temperature, or in this case 50. In the CHARMm dictionary, published by MSI, there is an example where the number of steps, STEPS is 3000, IHTFRQ is 50, and TEMINC is 5. Does this always hold, or am I goofy? In my run, I've set IHTFRQ to be 100 and this means that TEMINC would be 0.5. My NSTEPS are 10000. Are these values of IHTFRQ and TEMINC ok? Thanks in advance for your assistance. Cheers, Richard