On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote:
*Dear all,
I have been trying to generate pre-equilibrated ethanol
solvent box of 512 molecules in **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.*
You should follow the suggestions here
http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation. 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.
Mark
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