From chemistry-request@server.ccl.net Mon Sep 24 14:54:44 2001 Received: from unq.edu.ar ([200.49.110.238]) by server.ccl.net (8.11.2/8.11.0) with ESMTP id f8OIqk111531 for ; Mon, 24 Sep 2001 14:54:42 -0400 Received: from pii400win95.unq.edu.ar [200.49.110.145] by unq.edu.ar [200.49.110.238] with SMTP (MDaemon.PRO.v4.0.0.R) for ; Mon, 24 Sep 2001 15:49:03 -0300 Message-Id: <5.1.0.14.0.20010924153719.00a2a5e0@mail.unq.edu.ar> X-Sender: mlema@mail.unq.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 24 Sep 2001 15:42:28 -0300 To: chemistry@ccl.net From: =?iso-8859-1?Q?Mart=EDn?= Lema Subject: Temperature trouble Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-MDRemoteIP: 200.49.110.145 X-Return-Path: mlema@unq.edu.ar X-MDaemon-Deliver-To: chemistry@ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8OIsi111582 Dear CCLs: In my MD simulations, I start heating up the system using Berendsenīs algorithm and when it reaches 300 K I switch to Andersenīs. The thing is the average temperature of the system then stabilizes around 294 K. The system is a myoglobin of 2134 atoms (including hydrogens), implicitly solvated using the SASA algorithm and using the CHARMM27 parameter set. I have tried different collision frequencies for the thermostat, longer times, longer cutoffs, etc, but I canīt find the origin of this discrepancy. Collision values of 0 (which means no application of the thermostat) and 166 (which means velocity is reassigned for every atom in every step) renders the system at 300 K, but it is not the case for more reasonable values in the range 0.02 - 5. The trouble persist when performing the simulation in vacuo or using other solvation algorithms. Does someone figures out where the trouble is? clues are welcome at mlema@unq.edu.ar. Useful responses will be summarized. Martin Lema National University of Quilmes Argentina .