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

[Jae Hyun Park]

Thank you so much, Berk.
I deeply appreciate of your comments.

Jae H. Park

---- Original message ----
>Date: Tue, 11 Jul 2006 09:04:19 +0200
>From: "Berk Hess" <gmx3 at hotmail.com>  
>Subject: Re: [gmx-users] Question about center-of-mass 
removal  
>To: gmx-users at gromacs.org
>
>
>
>
>>From: Jae Hyun Park <jaepark at uiuc.edu>
>>Reply-To: Discussion list for GROMACS users <gmx-
users at gromacs.org>
>>To: Discussion list for GROMACS users <gmx-
users at gromacs.org>
>>Subject: Re: [gmx-users] Question about center-of-mass 
removal
>>Date: Tue, 11 Jul 2006 00:27:55 -0500
>>
>>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) ?
>
>Everything depends on if your system has an absolute 
reference
>in space, in Gromacs this can only be done with postion 
restraints
>or freeze groups.
>You have not written if this is the case.
>
>If there is no absolute reference, your com is uncoupled 
and you
>should remove the com motion.
>If you have an absolute reference you should not remove com 
motion
>as this will influence the sampling in the system.
>
>Fluid flow itself has nothing to do with this. If the fluid 
flows in one
>direction this is because of a force working on it and 
there should
>be an equally large reaction force working on something else
>in the opposite direction.
>
>Berk.
>
>
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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