From: Richard Wood (
Date: Thu Jul 10 2014 - 08:31:54 CDT

Can't you just write down the energies for each structure?


From: [] on behalf of Nuno Sousa Cerqueira []
Sent: Thursday, July 10, 2014 7:24 AM
To: Vmd l
Subject: vmd-l: pdb animation


I have a series of PDB structures that I have joined in order to create a trajectory.
I would like to see the animation of those PDB structure in VMD and at the same time observe the changes in energy of each structure.
One way of doing this is to store the energies of each PDB as a comment on the trajectory file. So each PDB will have a line with a comment containing its energy.
My question is: Is there any way that while VMD is playing the PDB animation I can retrieve the stored energies ( such as a variable=?
Does anyone has a idea of doing this ?




Nuno M. F. Sousa A. Cerqueira
Chemistry Department
Faculty of Sciences
University of Porto
Rua do Campo Alegre, s/n
4169-007 Porto
Tel: +351 220402501
Fax: +351 220 402 009