Re: [AMBER] stopping simulation in between

From: onetwo <>
Date: 2 Jul 2013 15:27:09 -0000

Dear Dan,

Thanks a lot for the reply.

Actually, i ran it in parallel giving all the processors to it to run.

now i have to run another simulation on it,thats why i wanted to stop the first one. otherwise finishing the previous job will still take 2-3 days on my system to be over. otherwise running two jobs together will not be a good idea otherwise.

Thanks for help.

On Tue, 02 Jul 2013 19:56:19 +0530 wrote


On Tue, Jul 2, 2013 at 7:22 AM, onetwo wrote:

> So, how can i stop the simulation in between. and the output will be *.rst file that we have to use for analysis.

There is no clean way to stop the simulation before it hits nstlim,

you have to kill it with kill -9 or something similar. Be aware

that if you happen to kill the simulation in the middle of a

trajectory write you could end up with a partial frame at the end, but

even worse if you happen to kill the simulation in the middle of

writing a restart you will not be able to restart the simulation, so I

would be very cautious in attempting this.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 02 2013 - 08:30:03 PDT
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