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

[Eric Jakobsson]

We sort of fell into dealing with this problem by accident.  We had never 
bothered to use c-o-m corrections with cutoffs, and it never seemed to 
matter, but when we went to PME this problem arose.

Eric

At 01:09 PM 3/4/2003 -0800, you wrote:

>>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.
>
>I haven't tested running PME without resetting the c-o-m motion a lot, but 
>this is probably the only area where problems are worse with PME than with 
>cutoffs. PME calculates the forces by numerical differentiation of the 
>interpolated potential, so the residual noise will be slightly higher than 
>with the pairwise forces calculated for cutoffs. (action and reaction 
>forces are not guaranteed to be exactly equal). nstcomm=1 should solve it 
>in any case!
>
>Cheers,
>
>Erik
>
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---------------------------------
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
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909