From: "Zhou Bo" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: <[email protected]>
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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