Re: velocity error

From: bo baker (bo.bybaker_at_gmail.com)
Date: Thu Jan 05 2006 - 18:02:35 CST

Hi, Peter,

I try to modify the .conf file as your suggested: delete the BoxCell
line, and increse the PME grid. But more atoms are moving too fast.
and
'FATAL ERROR: Bad global exclusion count!'.

I am not sure which part is wrong. I have included the .conf and .log
files as attachments.

Thank you for advice.

Bo

On 1/5/06, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> 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.
> Peter
>
> 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
> >attachments.
> >
> >Thank you for advices.
> >
> >Bo
> >
> >
>
'


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