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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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