Re: total energy stuck between two levels

From: Jérôme Hénin (
Date: Wed Jan 07 2004 - 02:42:33 CST

Hi Amit,

Are you using multiple timestepping? If yes, you should output energies with a
period that is a multiple of the slowest timestep (normally
fullElectFrequency). Otherwise, you may get incorrect energies.

I don't think this is explained in the NAMD manual, but maybe it should.


> Hi everyone,
> I have had this problem with the new namd version 2.5. Whenever I simulate
> peptide in water- first minimize the system and then start the production
> run- in the production run, the total energy oscillates beween two levels
> very far apart. I can not understand why?? Minimization seems to be
> perfectly fine. There was a suggestion to use separate thermostats for
> peptide and water. if this is the problem then how do you go about doing
> this? thanks,
> Amit.

Jérôme Hénin
Equipe Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS    UMR 7565
B.P. 239	54506 Vandoeuvre-lès-Nancy Cedex
Tel : (33) 3 83 68 43 95	Fax : (33) 3 83 68 43 71

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