From chemistry-request@ccl.net Mon Jun 6 18:23:51 2005 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j56MNksX002583 for ; Mon, 6 Jun 2005 18:23:47 -0400 Received: from laurence.mbi.ucla.edu (d-128-97-138-48.chem.ucla.edu [128.97.138.48]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id j56LiuKg005650; Mon, 6 Jun 2005 14:45:00 -0700 Message-Id: <6.1.2.0.2.20050606133823.03758108 {} po.chem.ucla.edu> X-Sender: lavelle {} po.chem.ucla.edu X-Mailer: QUALCOMM Windows Eudora Version 6.1.2.0 Date: Mon, 06 Jun 2005 14:43:50 -0700 To: amber {} scripps.edu, CHEMISTRY {} ccl.net From: Laurence Lavelle Subject: Protein dynamics. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net In looking at the dynamical motion of a protein, is Amber (Cornell et al. (1994) force field) (Amber 99 parameters) considered a reasonably realistic protein force field (or, as good as or better than most) ? In looking at the dynamical motion of a protein (for example using Amber), what are the pros and cons to doing Molecular Dynamics vs Langevin Dynamics vs Monte Carlo ? {Some will say it depends on the details (distance dependent dielectric vs explicit solvent water molecules, no cutoffs vs with switched or shifted cutoffs, with or without periodic boundary conditions, etc.). However I am hoping (in addition to the above two questions) to get a general sense of how realistic MD, LD and MC are with respect to illustrating protein motion. By protein motion I mean a folded protein in a constant temperature simulation (for example with a distance dependent dielectric, no electrostatic cutoffs, no periodic boundaries) and comparing the protein dynamics at different temperatures. To be explicit, I am not talking about protein folding or unfolding pathways.} Thanks, Laurence Lavelle