[gmx-users] Extended trajectory

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 21 23:20:34 CEST 2009

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:


Try with the syntax and naming convention given there (to avoid potential I/O 
confusion) and see if your run works.


> 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


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