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On 17/01/2011 6:25 AM, Marcelo Silva wrote:
<blockquote cite="mid:BAY125-W72FD86292088E40F191AAD4F50@phx.gbl"
type="cite">
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Hello everybody,<br>
<br>
I tried to run a simulated annealing protocol with 500 molecules
of perfluorohexane, trying to optimize their structure and keep on
with further equilibration.<br>
Since in the end of simulated annealing there were a lot of holes
in the NPT box, I've now tried to restrain the positions of the
perfluorohexane molecules using -DPOSRES (I've attached the mdp
file).<br>
</blockquote>
<br>
Sounds like you might need to check out FAQ #11.
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/FAQs">http://www.gromacs.org/Documentation/FAQs</a><br>
<br>
<blockquote cite="mid:BAY125-W72FD86292088E40F191AAD4F50@phx.gbl"
type="cite">The problem is that mdrun keeps running in background
but there's no output showing in the sa.log file. What could be
the problem?<br>
</blockquote>
<br>
File systems store I/O in temporary areas in memory, and only write
periodically.<br>
<br>
Mark<br>
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