[gmx-users] NVT equilibration of Ethanol in OPLSAA.

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 4 10:31:36 CEST 2011

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.

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