From chemistry-request@server.ccl.net Sat Jun 10 15:31:35 2000 Received: from mallard.duc.auburn.edu (mallard.duc.auburn.edu [131.204.2.11] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA27492 for ; Sat, 10 Jun 2000 15:31:35 -0400 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id OAA18251 for ; Sat, 10 Jun 2000 14:31:35 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Sat, 10 Jun 2000 14:31:35 -0500 (CDT) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: T1-diagnostic Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's It is known that T1-diagnostic is used to determine whether single determinant wavefunctions can decribe molecular system properly or not. Could anybody give more details about T1-diagnostic such as how to calculate and how to apply? I will summarize it. Thank you in advance. yours Ohyun Kwon Department of Chemistry Auburn University Auburn, AL, 36849 From chemistry-request@server.ccl.net Sat Jun 10 14:43:37 2000 Received: from mailhost.rdg.ac.uk (exim@sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA27234 for ; Sat, 10 Jun 2000 14:43:36 -0400 Received: from suma3 ([134.225.16.13] helo=suma3.rdg.ac.uk) by mailhost.rdg.ac.uk with esmtp (University of Reading Email Service) id {130qEK-0004mE-00} for chemistry@ccl.net; Sat, 10 Jun 2000 19:43:36 +0100 Received: from localhost (ssr97lrc@localhost) by suma3.rdg.ac.uk (8.8.8+Sun/8.8.8) with ESMTP id TAA15419 for ; Sat, 10 Jun 2000 19:43:36 +0100 (BST) X-Authentication-Warning: suma3.rdg.ac.uk: ssr97lrc owned process doing -bs Date: Sat, 10 Jun 2000 19:43:36 +0100 (BST) From: ssr97lrc X-Sender: ssr97lrc@suma3 To: CCL Subject: Molecular Dynamics Vol, Perssure & Density issues In-Reply-To: <3940A270.D1B0691B@uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8BIT dear all, i'd like to run a series of md experiments at various temperatures; 298 and 398k using gromacs2 in both cases the pressure of the solvent bath is set to 1 atm at the start of unrestrained md but averages -1.4 atm during the 298k run and 10.7atm during the 398k run, density fluctuates around 1.0 kg/l in both runs. >from a paper by daggett et al i have gleaned that densities should be are altered in md solvent bath simulations to compensate for increased temperature ie a 498k simulation would be conducted with density ~0.8kg/l, i think. that calculation is referenced to a paper i cannot obtain at present. ****so at what density should a 398k simulation be conducted at and how is that calculated considering water must stay in liquid phase? will summarise ¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` /=\Mr. Lee R. Cooper MSc, P.E.D.A.L, Dept.of//=\ =// Comp. Science, University of Reading, Whiteknights\=// //=\ PoBox 225, Reading, Berkshire. RG6 6AY (UK) //=\ °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` From chemistry-request@server.ccl.net Sat Jun 10 13:52:27 2000 Received: from mailhost.rdg.ac.uk (exim@sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27078 for ; Sat, 10 Jun 2000 13:52:22 -0400 Received: from suma3 ([134.225.16.13] helo=suma3.rdg.ac.uk) by mailhost.rdg.ac.uk with esmtp (University of Reading Email Service) id {130pQU-0003qO-00} for chemistry@ccl.net; Sat, 10 Jun 2000 18:52:06 +0100 Received: from localhost (ssr97lrc@localhost) by suma3.rdg.ac.uk (8.8.8+Sun/8.8.8) with ESMTP id SAA13824 for ; Sat, 10 Jun 2000 18:52:06 +0100 (BST) X-Authentication-Warning: suma3.rdg.ac.uk: ssr97lrc owned process doing -bs Date: Sat, 10 Jun 2000 18:52:06 +0100 (BST) From: ssr97lrc X-Sender: ssr97lrc@suma3 To: CCL Subject: free modelling software In-Reply-To: <3940A270.D1B0691B@uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8BIT dear all, could anyone name a free modelling package for win98 or redhat linux which does all of the following things; o handles pdb files cleanly o has full atom typing capabilities o allows you to sketch/build covalently modified cys, lys or n-term residues o select & clean (with conjugate grad min) the modified residue o (re)name the added atoms of course msi's cerius2 software does three of these things but it does not fulfil the first criterion ¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°` /=\Mr. Lee R. Cooper Bsc(Hons) MSc, P.E.D.A.L, Dept.of//=\ =// Comp. Science, University of Reading, Whiteknights\=// //=\ PoBox 225, Reading, Berkshire. RG6 6AY (UK) //=\ \=// Tel +44 (0)118 987 5123 x7645 (0915-1700)|Fax \=// °¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`´°¤ø,¸¸,ø¤°`