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

[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.