VMD-L Mailing List

From: nadiav_at_soton.ac.uk
Date: Fri Sep 08 2006 - 07:55:42 CDT

Dear VMD users,

I am trying to view my normal modes calculated in Nmode(amber9). I
understand that the IED plug-in (VMD-1.8.2) can display the modes, providing
the vector file is given the .pev extension.

I have used IED before for small molecules to display the modes and had no
problem, however now I am trying to view the modes of a large protein
system (4962 atoms). When the Eigenvectors are loaded, I can only see very
vague movements. I was wondering if there is anything I need to do to the
files before viewing them in IED apart from changing the vector file
extension.

For example I know that if you are viewing an eigenvec.trr file from GROMACS
ones needs to add a box of 1 1 1 to the vectors. Is there an equivalent
routine for vector file from Nmode?!

Thank you,

Nadia Vahdati
J.W.Essex group
Southampton, UK