RE: possible bug with NAMD Energy plugin

From: Zumot, Elia Nabil (
Date: Tue Aug 31 2010 - 18:00:17 CDT

Hi again,

In order to "trick" NAMD, and to avoid having to wait about 30 minutes to calculate the interaction between the substrate and protein (dcd file of just 50 frames) upon using the "update selections every frame" I have used "protein and same residue as pbwithin 200 of substrate" in the second selection box with "update selections" off. This way I get to include the periodic boundary conditions without having to update the selection every frame.
Here I get the same results of interaction energy regardless of whether "update selections every frame" is clicked on/off.

However, I still get some very high interaction energy values (up to 1'000'000) when the substrate but not the protein crosses the periodic cell boundry (and these values are the same regardless of whether the selections are updated or not).

Is there a way around it?
And is there a way for running interaction energy calculation with the selections updated without having to generate a pdb/dcd file for every frame as NAMDEnergy does (which consumes a lot of time)?

Thanks in advance


From: Peter Freddolino []
Sent: Monday, August 23, 2010 7:58 PM
To: Zumot, Elia Nabil
Subject: Re: namd-l: possible bug with NAMD Energy plugin

Hi Elia,
periodic boundary conditions will only be taken into account if you use pbwithin instead of within in your atom selection text -- this is simply the proper way to use the vmd atom selection language. Please let me know if you still have difficulty after fixing your atom selection text.

On 08/23/2010 04:19 PM, Zumot, Elia Nabil wrote:
Hi all,

I'm calculating the energy of interaction between the ubstrate and protein residues within a radius of 5A around it under PBC in an NPT ensemble using the NAMD-Energy plugin.
The protein together with the substrate move and cross the boundry only they do not do so at the same time and at the same frames so at certain frames the protein could be at one end of the cell and the substrate on the other even though the substrate is still bound at the core of the protein.

The problem arises at these points where I get an energy of interaction that is equal to 0.0. Is this a bug with the pluging or is there a way around it?

I have the "PME" and "update selection every frame" options clicked when I carry out the calculation and VMD/NAMD are the latest versions.

Thank you in advance


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:06 CST