From: Javad Azadi (
Date: Tue Jul 04 2006 - 11:14:36 CDT


I am using VMD to analyze 6ns trajectories produced in gromacs and it is proving to be very slow. I am
using a MacBook 2.0Ghz base model for this task, but I don't know if it is my system that is to blame. I
want to measure the distance between two sets of two atoms (distance between atom1-atom2 and the
distance between atom3-atom4) and the dihedral formed by the atoms (atom1-atom2-atom4-atom3).
Loading the trajectory takes a while, then going to the label menu and saving the plot also takes a
while. I can do one trajectory every half-hour with the current method, but is there a faster way using

Javad Azadi
Undergraduate Researcher
The Ohio State University