From: Austin B. Yongye (ybausty_at_yahoo.com)
Date: Thu Jan 28 2010 - 12:28:37 CST
I am running a simulation for a solute in a box of trichloromethane under NPT conditions. I tried:
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:
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.
PS. I am using the namd binary in the NAMD_2.7b2_Linux-x86 distribution.
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