[gmx-users] Regarding Density

Dallas Warren Dallas.Warren at monash.edu
Sun Oct 9 23:08:18 CEST 2011

Well, yes that will scale the box size to give a certain density.

However, if that is not the correct number of molecules for that particular solvent model, under the conditions you run it, then with NVT you will end up with voids and a negative pressure, and with NPT the box size will decrease until it reaches the appropriate density.

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: Friday, 7 October 2011 8:02 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding Density

Dear All,
             Please somebody tell me in what way the gromacs calculate the density for given no. of molecules and volume of the box. I generated solvent box using genbox_d command line. Is it right that I can scale the solvent box according to density of my interest after generating box using genbox_d command line?

With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

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