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On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote:
<blockquote
cite="mid:CA+c-nQzm-ipTRZVjiWUqyA7YLT-Zafniw+_iBy5XSNcaNJJsQg@mail.gmail.com"
type="cite"><b>Dear all,<br>
I have been trying to generate pre-equilibrated
ethanol solvent box of 512 molecules in </b><b>OPLSAA ff. I
used ethanol.itp in oplsaa.ff directory for generating the
topology file for ethanol. After NVT equilibration some of the
molecules get aggregated and there is some void in the box. I
tried running at faster time scales like 0.2 fs then also I was
getting the same. Please help me to overcome this problem.</b><br>
</blockquote>
<br>
You should follow the suggestions here <a
href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a>.
Even if you have, we'd need a lot more detailed information about
your procedure and parameters to be able to guess what might have
gone wrong.<br>
<br>
Mark<br>
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