Re: possible bug with NAMD Energy plugin

From: Peter Freddolino (
Date: Mon Aug 23 2010 - 18:58:26 CDT

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
> Elia

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:04 CST