Re: Water Box Shape Changing during NVT Simulation!

From: Jeffrey J. Potoff (
Date: Mon Mar 08 2010 - 15:05:10 CST

Ronald Salesky wrote:
> Hi Aditya,
>>> My question also is whether the volume can still remain the same
>>> even with the shape of the water box changing to cylindrical? Does
>>> an NVT simulation place a restriction on the shape or just the total
>>> volume of the water box. If its just the volume, cant the water
>>> molecules just arrange and rearrange themselves without the volume
>>> changing but just the shape?<<
> My understanding is the PBC (periodic boundary condition) you have
> placed on your system sets a periodic cell with the x,y,z boundaries
> you have specified, which means the system is modeled as if it is
> really a periodic array of the same protein/solvent system like in a
> crystal. Since the solvent/protein system wants to converge to its
> minimum energy, the solvent shape within the cell will change. If you
> were to just model a single cube of water with no solute molecule it
> would seek its minimum energy state which would be spherical. I am
> learning NAMD/VMD as you are, so those more experienced may disagree
> with some of these points.
Just a point of clarification. In a canonical (NVT) MD simulation, one
is minimizing the free energy of the system, not the energy.

Jeffrey J. Potoff               
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815

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