From chemistry-request@server.ccl.net Thu Mar 6 12:13:45 2003 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h26HDha20922 for ; Thu, 6 Mar 2003 12:13:43 -0500 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id SAA04395 ; Thu, 6 Mar 2003 18:12:33 +0100 (MET) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen To: CHEMISTRY@ccl.net Subject: Re: CCL:Energy conservation of molecular dynamics in the presence of electrostatic forces Date: Thu, 6 Mar 2003 18:11:12 +0100 User-Agent: KMail/1.4.3 References: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> In-Reply-To: <5.1.1.6.2.20030306081753.00b185a8@secure.concord.org> Cc: Charles Xie MIME-Version: 1.0 Message-Id: <200303061811.12617.hinsen@cnrs-orleans.fr> X-MailScanner: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h26HDla20923 On Thursday 06 March 2003 15:20, you wrote: > Problems, however, arise when molecules are charged. Because > electrostatic forces are much more long-ranged (1/r dependence) and > typically stronger, the magnitude of electrostatic forces on atoms can > be several hundred (or even thousand) times greater than that of van > der Waals forces. As a result, the time step has to be accordingly > reduced for two or three orders of magnitude, in order for the total > energy to conserve. This means a time step of 0.001-0.01 femtosecond > has to be applied. That doesn't seem quite right. A long range does not imply a strong force, it just means that the force on any given atom depends on the positions of many others. The contributions can (and often do, in practice) cancel out. Moreover, large forces do not automatically imply fast motions, other parameters (e.g. temperature) enter as well. You don't say what kind of systems you study. In liquids and biomolecules at room termperature, a time step of 1 fs works perfectly well with electrostatic interactions. One does see improvement of energy conservation when going to 0.5 fs, but there is no need to go to time steps as small as those you quote. So either your system is very different, or there is a bug in your force calculation code. > Energy conservation is generally not an concern for most classic molecular > dynamics simulations that assume a heat bath (for controlling the > temperature to a desired value, thus remove the numerical errors resulted > from large a*dt^2). That depends on the thermostat that is used. Personally I prefer the extended systems method, precisely because there is still a conserved energy that can be used to monitor the behaviour of the simulation. -- ------------------------------------------------------------------------------- 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 -------------------------------------------------------------------------------