RE: possible bug with NAMD Energy plugin

From: Zumot, Elia Nabil (
Date: Tue Aug 24 2010 - 12:15:35 CDT

Problem solved.
Thank you Peter.



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


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