Re: Solute moves outside of solvent box

From: Jeffrey J. Potoff (
Date: Thu Jan 28 2010 - 12:55:08 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 ( 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.
A bubble in the center of your box suggests you don't have enough
solvent molecules to start with, although it's hard to know for sure
without seeing your input files. What is your initial box size, number
of solute molecules, and target density? How big is the solute?

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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