Re: problem with water

From: Jeffrey J. Potoff (
Date: Tue Aug 24 2010 - 11:55:44 CDT

Swarna M Patra wrote:
> Hi Namd users
> I am running a protein+lipid bilayer +water simulation (NVT) at zero
> temp.. After minimization, the protein has restrain of 500 kcal and
> water from one side is vanishing and adding to the other side . I am
> using wralpAll option. cutoff is 10 and pairlist is 12.5 and switch
> dist is 8.5. when I look into the water molecules i see patches of
> hole(no water). pl help me , what could be the possible reason and
> which parameter i need to adjust.
> thanks
> swarna
If you have holes with no water, most likely you don't have enough water
in the simulation to begin with. Because of the lipid bilayer, the
simulation cell cannot adjust to achieve the correct water density.
Instead, you get holes and the water condenses. Make sure you have
enough water to give you a density of 1 g/cm^3.

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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