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

2013-11-12 Thread arun kumar 
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.

Thanking you.

-- 
Arun Kumar Somavarapu
Project-JRF
Dr. Pawan Gupta's lab
Protein Science and Engineering Dept,
Institute of Microbial Tecnology,
Sec 39-A, Chandigarh - 160036.
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Re: [gmx-users] Restarting a simulation after replacing an empty md.trr file

2013-11-12 Thread 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

--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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