Re: Solute moves outside of solvent box

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Tue Feb 02 2010 - 10:26:09 CST

Austin B. Yongye wrote:
> Dear all:
> I am running a simulation for a solute in a box of trichloromethane under NPT conditions. I tried:
> wrapAll on;
> wrapAll on and wrapNearest on;
>
> but the solute keeps drifting outside of the box. This posting (www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/9885.html) indicates that unless there's a bubble in the system, there should be no concerns. However, in my case a bubble is created at the center of the box.
>
> Finally, I tried:
> wrapNearest on
>
> and the solute stayed in the box. But this option changes the shape of the box (as mentioned in the manual). I am sure changing the box from cubic to hexagonal will affect the vdW and electrostatics via PME and non-bonded cutoffs, and image distances.
> Any suggestions on how to keep the solute at the center of the box will be appreciated.
>
> Thanks,
> Austin-
>
> PS. I am using the namd binary in the NAMD_2.7b2_Linux-x86 distribution.
>
>
Dear Autstin,
    Based on the information you provided, 54x54x54 box, 955 chloroform
molecules and a solute of 4200 Ang^3, you probably don't have enough
solvent in the box. Based these numbers, you should have a solvent
density of 1.24 g/cm^3, which seems ok, except that the density of
chloroform at room temperature is around 1.48 g/cm^3. You need roughly
another 200 solvent molecules to make this work.

If you did not have a large solute, the system would naturally shrink to
the correct density. However, the presence of a large solute limits
what the simulation can do in terms of shrinking the box, resulting in
the "bubbles" you see. Hope this helps.
Jeff

-- 
======================================================================
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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