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.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Kumar Venkatraman Sent: Tuesday, 4 October 2011 6:17 PM To: gmx-users@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, INDIA.
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