[gmx-users] Question about center-of-mass removal

Jae Hyun Park jaepark at uiuc.edu
Tue Jul 11 07:27:55 CEST 2006

Thank you, Mark.

I have one more question for the confirmation. So, if there 
is other asymmetries (e.g. initially the fluid is at one 
side and the other side is empty, and as time goes on, it 
spreads to the empty side - non-equilibrium process. In flow 
direction there is no periodicty while periodic in other two 
directions), do I have to turn off the center-of-mass 
removal (e.g. nstcomm = 0) ? 

Thank you in advance for your kind consideration.

Jae H. Park

---- Original message ----
>Date: Tue, 11 Jul 2006 10:09:50 +1000 (EST)
>From: "Mark Abraham" <mark.abraham at anu.edu.au>  
>Subject: Re: [gmx-users] Question about center-of-mass 
>To: "Discussion list for GROMACS users" <gmx-
users at gromacs.org>
>> Dear all;
>> I have very simple question about center-of-mass removal,
>> which would be very easy for the expert like you.
>> When we dealing with the system whose center-of-mass is 
>> (e.g. initially the fluid is at one side, and as time 
goes on,
>> it spreads to other direction), do we still have to 
remove the
>> center-of-mass motion (e.g. nstcomm = 1) ?
>Unless you're building in some other asymmetry, your 
diffusion will be in
>both directions, so your COM motion should still be zero. 
You can see this
>clearly if you consider the separate COM of your two 
fluids - they aren't
>changing on average. Thus I guess that enforcing COM is 
probably OK.
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Jae Hyun Park, Ph.D.
Postdoctoral Associate
3221 Beckamn Institute
University of Illinois at Urbana-Champaign
405 North Mathews Avenue
Urbana, IL 61801
(Tel) 217-244-4353, (FAX) 217-244-4333
(E-mail) jaepark at uiuc.edu

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