VMD-L Mailing List

From: Surjit Dixit (surjit_at_lctn.u-nancy.fr)
Date: Mon Sep 11 2000 - 13:54:16 CDT

Hi,
I have been trying to visualize some trajectories generated by CHARMM (academic) with some
constraints in the system using VMD1.6a1. I wish to report an odd behaviour by VMD (vmd1.4 behaves
the same way too). My system is a protein solvated in water and the trajectory is from a run where the
protein is frozen and the waters are being equilibrated. VMD for some reason does not show any of the
waters as moving at anytime throughout the trajectory. My dynamics simulations and trajectory seems to
be fine, I have confirmed this by reloading the trajectory within charmm itself for analysis and have also
visualized the trajectory with gOpenMol. VMD is able to show the moving configurations in the trajectory
when no constraints are involved in the simulation.
I wonder if anybody has noticed anything like this?
I like the new interface of VMD, its more pleasant, thanks.
Best regards,
Surjit 
-- 
Surjit B. Dixit, Ph.D.                    Email: surjit@lctn.u-nancy.fr 
Laboratoire de Chimie Théorique, U.M.R. C.N.R.S. #7565, B.P. 239        
Université Henry Poincaré-Nancy I, 54506 Vandoeuvre-lès-Nancy, France
Phone: 33-3-83.91.20.00 Extn:3588         Fax: 33-3-83.91.25.30