From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Wed Jan 04 2006 - 17:46:46 CST
I don't know if there is any point in the system that is overheated.
One suggestion would be to minimize the system for about 100 fs or more when you restart from 22000. After this minimization, the simulation would continue.
Try to see if any bond, angle or dihedral is distorted.
Boyang
bo baker <bo.bybaker_at_gmail.com> 写道： Hi, the periodic box is about:
22000 76.154 0 0 0 74.2013 0 0 0 79.083 25.5 37 23.3 -3.78574e-06
-3.78574e-06 -3.78574e-06 0 0 0
at 22000 step, which is the starting for the next MD run. And I set
the cell basis vectors as:
cellBasisVector1 78.00 00.00 00.00
cellBasisVector2 00.00 76.00 00.00
cellBasisVector3 00.00 00.00 81.00
cellOrigin 25.5 37.0 23.3
margin 5
Pme on
PmeGridsizeX 78
PmeGridsizeY 76
PmeGridsizeZ 81
Thank you for any suggestions.
Bo
On 1/4/06, Boyang Wang
wrote:
> Hi. Can you check if your periodic box has enlarged?
> If your box becomes bigger, the previous cell basis vectors are too small,
> and this may be one of the reasons your have too fast moving atoms.
>
> best,
> Boyang
>
> bo baker 写道：
> 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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