Re: Water Box Shape Changing during NVT Simulation!

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
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.

-- 
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Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
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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