[gmx-users] Fw: the crashed run

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Mon Dec 9 07:41:44 CET 2013

thanks for your reply
Have a Great Day

On Monday, December 9, 2013 1:35 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 12/8/13 6:59 AM, Mahboobeh Eslami wrote:
> thanks for
 your reply
> please suggest the best command for restart a crashed run.
> i use following command
> mdrun -v -deffnm md -cpi md
> is this command good or not?

If the desired .cpt file is md.cpt, then mdrun -deffnm md -cpi suffices.  If you 
need a previous .cpt file (i.e. md_prev.cpt), then you must specify its name 
explicitly.  Depending on why the run crashed, simply restarting may not be 
worthwhile.  If the crash was due to the system blowing up, it is a waste of 
time and you should investigate the crash.  If it was a hardware failure, disk 
error, etc. then continuing from a checkpoint is fine.


> thanks
> On Sunday, December 8, 2013 2:18 PM, "jkrieger at mrc-lmb.cam.ac.uk" <jkrieger at mrc-lmb.cam.ac.uk> wrote:
> _prev.cpt might be ok. I think it writes those in case the current cpt causes problems
> On 8 Dec 2013, at 09:57, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
>> hi GMX users
>> i use
>   gromacs 4.6.3 double precision for protein
 ligand complex during the 20 ns. my run crashed, I'm not
>   sure that restart my run from cpt file or run a new production.
>> is the result of  started again run a reliable like a non crashed run.
>> thanks for your help
>> --
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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