[gmx-users] AFM Pulling and com motion

[Zhou Bo]

   Thanks for your reply. There is no absolute reference here. The system is
just from this web site
"http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007"
(hands-on: The pull package).
 I really do not know the advantage or necessity of stopcm in SMD, because
when I test the two systems, 
with and without stopcm, there is a distinct difference between the
calculated pull force.

>You didn't tell if you are using an absolute reference or not.
>With an absolute reference you should not remove the com motion.

>Berk.

>>From: "Zhou Bo" <homeboyzb at gmail.com>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: <gmx-users at gromacs.org>
>>Subject: RE: [gmx-users] AFM Pulling and com motion
>>Date: Thu, 20 Sep 2007 22:44:29 +0800
>>
>>   Thanks to Berk. I just tested two system, one with stopcm and the other
>>without stopcm. I calculated the pull forces and compared them with each
>>other. There are really some distinct differences between them during the
>>80ps simulation. I worry about it, for example, in long time simulations, 
>>so I want to know which one is the better and reliable choice, stopcm or
>>without stopcm. As I know, the NAMD package only removes the initial
center
>>of mass motion.
>>Thanks for your reply.
>>
> >>Hi GXM Users,
> >>    I'm trying to execute some AFM Pulling. I followed the pull code
>tutorial
> >>from GMX WORKSHOP 2007, and I found there is no specific to com motion 
>in
> >>mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was
> >>confused about it as I believed we should not stopcm when doing AFM
>Pulling
> >>because of the external force. Does it problematic to stopcm when doing
>AFM
> >>Pulling?
> >>
> >>Thanks!
> >>
>
> >This depends on what type of pulling you are doing.
> >If you have an absolute reference you are right.
>
> >But when you pull between two groups of atoms, there are no
> >external forces, but internal forces between two groups.
>
> >Berk.
>
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End of gmx-users Digest, Vol 41, Issue 73
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