Volume of the Solution used for MD simulation

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Thu Mar 04 2010 - 06:32:57 CST

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Hi,

Is there a way I can calculate the volume of the system and the
concentration of the protein in the water box ,being studied by Molecular
Dynamics Simulation.Is there any formula by which I calculate the same using
the number of waters in the solvent box and the number if peptides.
Also, is it necessary to use a two-step equilibration with restraints placed
on the peptide in one step. Is there need for any restraints to be placed on
the peptide during the slow heating step? I generally use an increment of
0.001K per step for the slow heating of the system.

Thanks,

Srivastav R
Junior Research Assistant,
Dept of Biosciences and Bioengineering,
IIT Bombay, Mumbai-400076
Maharashtra, India

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