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

Dallas Warren Dallas.Warren at monash.edu
Tue Oct 4 23:17:40 CEST 2011

Sounds very much like you have an insufficient number of molecules in the box to fill it up.  If you look at the pressure data for the simulation, I suspect you will find that it is negative, the box wants to decrease in volume.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Ravi Kumar Venkatraman
Sent: Tuesday, 4 October 2011 6:17 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] NVT equilibration of Ethanol in OPLSAA.

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.

With regards,
Ravi Kumar Venkatraman,
IPC Dept.,
IISc, Bangalore,
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