From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
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.
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 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 http://potoff1.eng.wayne.edu ======================================================================
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