[gmx-users] RE: NVT EQUILIBRATION
Dallas.Warren at monash.edu
Thu Oct 6 00:42:15 CEST 2011
Keep the discussion to the emailing list please.
How many molecules that is required you can calculate yourself. What is the density? You know the volume, therefore you can calculate yourself how many molecules should be in that space, simple calculation. You should also be able to eye ball based on the coordinate file you mentioned that was full of voids. If the voids take up about half of the box, you need roughly double the number of molecules, quarter, then you need 33% more. Plus, you can do it via trial and error, but the density calculation is the way to go.
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: Ravi Kumar Venkatraman [mailto:ravikumarvenkatraman at gmail.com]
Sent: Wednesday, 5 October 2011 7:48 PM
To: Dallas Warren
Subject: NVT EQUILIBRATION
Dear Dallas Warren,
Yes you are right. Pressure was going negative when I did NPT equilibration. So increasing # of molecules will help me. If at all tell me how many molecules I should have approximately.
Thank you for your help.
Ravi Kumar Venkatraman.
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