Thanks allot for all your help
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
Hi,
I'll be most thankful if someone could tell me how to run a
fragmented trajectory using only the mdrun command. As of now I'm
using :
while(SimuTime < SimTime)
{
...
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o
run.tpr");
system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v
-deffnm run");
....
}
When I ran the above mdrun command alone, the run got stack
No error message? Just stuck? It could be that you're trying to read
and write to the same file names. I think your method of preparing
the extended run is also malformed, since the advent of checkpoint
files. See here:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Try with the syntax and naming convention given there (to avoid
potential I/O confusion) and see if your run works.
-Justin
Thanks
Arik
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