[gmx-users] Re: gmx-users digest, Vol 1 #653 - 10 msgs

[Eric Jakobsson]

This is a particularly egregious problem with PME.  We published on this in 
J. Comp. Chem. a couple of years ago.  It is the "flying ice cube" 
effect--as the translational motion builds up the heat bath keeps v squared 
the same so the temperature goes down, and if you let it go you have an ice 
cube hurtling through space very fast.

As Erik says, the solution is to keep resetting the center-of-mass motion 
to zero.

Eric

At 09:30 AM 3/3/2003 -0800, you wrote:

>>Here when I want to simulate molecules in water, using PME, I found that
>>all the system including waters, solutes have translational motions
>>building up. The system is moving faster and faster.
>
>That is a well-known artefact in all types of MD simulation; it comes from 
>the small rounding errors in the forces building up an acceleration.
>
>By default, Gromacs (as most other programs) removes this motion every 
>step, so check the value of nstcomm you're using in the mdp file!
>
>(you might have disabled it by mistake).
>
>Cheers,
>
>Erik
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the www 
>interface or send it to gmx-users-request at gromacs.org.

---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909