[gmx-users] AFM Pulling and com motion

[Berk Hess]

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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