[gmx-users] Restarting a simulation after replacing an empty md.trr file

[Justin Lemkul]

On 11/12/13 1:15 AM, arun kumar wrote:
> Dear Gromacs users,
>
> I am running a 50ns simulation of a protein having nearly 700 residues on
> 60 threads (Gromacs 4.6.3).
> At one point i got a disk space problem, so i have deleted the md.trr file
> and created an empty md.trr file. when i tried to restart the simulation
> from check point file on 100 threads, [ mdrun -v -deffnm md -cpi md.cpt -nt
> 100 ]
> i am getting a note and an error as fallows
>
> Reading checkpoint file md.cpt generated:
>    #PME-nodes mismatch,
>      current program: 100
>      checkpoint file: 60
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
> ...
>
> Source code file: checkpoint.c, line: 1767
> Fatal error:
> Can't read 1048576 bytes of 'md.trr' to compute checksum. The file
> has been replaced or its contents has been modified.
>
> please help me in overcoming this problem.
>

Use -noappend.  If you mess with any of the files that mdrun produces, the file 
appending procedure (which is the default behavior) will fail.

-Justin

-- 
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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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