[gmx-users] Re: I want to stop my run

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Dec 12 14:38:22 CET 2012

> On Wed, Dec 12, 2012 at 10:26 AM, Ali Alizadeh <
> ali.alizadehmojarad at gmail.com> wrote:
>> Dear All users
>> How can i stop my mdrun before it reaches to final step?
>> My mdrun will finish tomorrow but my system is turned off  today,
>> How can i get completely output files( .gro , .xtc , .trr )?
>> Can i analyze my simulation when my run is killed?
>> --
>> Sincerely
>> Ali Alizadeh

Dear Ali Alizadeh -

Yes, you can analyze your system. Even you can do this, if your system
is running.

But if you just terminate the mdrun process immediately, you may get
an incomplete last coordinates/energy frame.

There are many scientific software, which have a parameter key, which
is read at each time-step. If certain value is found for this key,
than the run stops correctly at the very next iteration. I am not
aware if gromacs has such a mechanism, as well as I do not think it
would be widely used.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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