Re: velocity error

From: Peter Freddolino (
Date: Thu Jan 05 2006 - 13:38:13 CST

Hi Bo,
if you are running a restart, you should not respecify the periodic
system; this is updated by the restart.xsc file. So you should comment
those lines out of the restart conf file. Also, it is generally not a
good idea to cut things to close to 1 point per angstrom on the PME grid
density. You should always allow a little extra just to be sure that you
won't go under 1 point per angstrom (this isn't a magical boundary, but
it is generally helpful to be able to specify a minimum density when
discussing your results). I would recommend padding your PME grid sizes
a bit more. These two changes may help; it is very possible that
respecifying the wrong periodic cell dimensions on restart caused part
of the system to wrap into itself.

bo baker wrote:

>Hello, NAMD:
>I try to run the MD without any restrains on. But I got the following
>error messages:
>ERROR: Atom 1804 velocity is 12661.2 -18890.9 10218.8 (limit is 5000)
>ERROR: Atom 1812 velocity is -12579.2 19072.4 -10061.2 (limit is 5000)
>ERROR: Atoms moving too fast; simulation has become unstable.
>ERROR: Exiting prematurely.
>The coordinates were from the prievious runs ( 20 ps of
>equilibration). I have included the .conf and .log files as
>Thank you for advices.

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