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Thanks allot for all your help <br>
<br>
Arik<br>
<br>
Justin A. Lemkul wrote:
<blockquote cite="mid:4ADF7B22.2070608@vt.edu" type="cite"><br>
<br>
Arik Cohen wrote:
<br>
<blockquote type="cite">Hi,
<br>
<br>
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 :
<br>
<br>
while(SimuTime < SimTime)
<br>
{
<br>
...
<br>
system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o
run.tpr");
<br>
system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v -deffnm
run");
<br>
....
<br>
}
<br>
<br>
When I ran the above mdrun command alone, the run got stack
<br>
<br>
</blockquote>
<br>
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:
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a>
<br>
<br>
Try with the syntax and naming convention given there (to avoid
potential I/O confusion) and see if your run works.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Thanks
<br>
<br>
Arik
<br>
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</blockquote>
<br>
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