Re: Solute moves outside of solvent box

From: Jeffrey J. Potoff (
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 ( 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.

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:44 CST