PME pair interaction analysis

From: Holly Freedman (
Date: Sun Jun 25 2006 - 16:17:41 CDT


Id like to use the pair interaction utility of NAMD to analyze a periodic
trajectory that Ive created using AMBER, and I want to get your input as
to whether this is possible. This is my first time using NAMD.
Specifically I want to calculate the PME periodic interaction between two
groups of atoms in the system. My plan is to first convert the trajectory
to the CHARMM dcd format with AMBER, and then write an NAMD config file
that reads the AMBER topology file and analyses the trajectory. The
trajectory was created under the condition of constant pressure and so my
question is whether the pair interaction analysis will, first read the box
information from the trajectory, and second, be able to apply PME to find
periodic interactions. I would really appreciate you getting back to me
on this with any help.

Thanks in advance,
Holly Freedman
postdoc, University of Alberta

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