VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 14:03:48 CDT

Hi,
  I'm forwarding your message to Peter Freddolino and Jim Phillips
since they apparently didn't see this email yet. They are the
experts on namdenergy and NAMD xsc files etc.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 12, 2007 at 06:10:14PM -0500, Alessandro Cembran wrote:
> Hi,
>
> I've been trying to use the VMD (v. 1.8.5 for Linux) on a hexagonal
> system ("WrapAll yes" and "WrapNearest yes") and, even if I feed VMD the
> correct .psf, .xsc and parameter files, I get the wrong electrostatic
> energy and a huge (i.e. 1E+8) VdW energy (while all the other energies
> match the NAMD ones).
> If I turn off PME and .xsc, then the VdW energy drops to a "normal"
> value, but of course a wrong one, since there are no images anymore. I
> checked the cell angles with "molinfo top get alpha" (beta, gamma) and I
> got the right 90.0, 90.0 and 60.0 values.
> I also tested the same plugin on a small water cubic box, and in this
> case everything works perfectly, Electrostatic and VdW energies match
> those obtained with NAMD.
> I am wondering if I have to set something special to have the NAMD
> Energy tool to recognize the hexagonal cell correctly.
>
> Thank you in advance,
>
> Alessandro
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078