[gmx-users] AFM Pulling and com motion

[Berk Hess]

>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: Fri, 21 Sep 2007 00:49:21 +0800
>
>    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.

MD is chaotic, so changing any detail will change the course of the 
simulation.
Any ensemble averages should be the same, but for short runs, as the course 
example, you do not reach the ensemble average.

I guess this is the reason for the difference.

Berk.

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