Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed)

From: David Case <>
Date: Fri 8 Nov 2002 23:17:18 -0800

On Fri, Nov 08, 2002, Miguel de Federico de la R?a wrote:
> I'm running a molecular dynamic simulation, and in the output file, I have
> found repeatedly one "suspicious" message.
> check COM velocity, temp: 0.000000 0.00(Removed)

COM stands for "center of mass": you asked the system to periodically remove
center-of-mass motion (see the nscm variable). Under most circumstances
this is not really necessary, since (if the system starts with no center of
mass motion) there are no forces that should create it. But round-off error
and other problems can sometimes creep in. As the message above shows, your
system has no center of mass velocities greater than 1 x 10**-6, which is

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Fri Nov 08 2002 - 23:17:18 PST
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