VMD-L Mailing List

From: Alessandro Cembran (cembran_at_chem.umn.edu)
Date: Mon Mar 12 2007 - 18:10:14 CDT

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