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.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: Friday, 7 October 2011 8:02 PM
To: gmx-users@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.
+91-9686933963.
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