Re: PME pair interaction analysis

From: Peter Freddolino (
Date: Sun Jun 25 2006 - 16:35:34 CDT

Hi Holly,
as long as you're using a 2.6 series version of NAMD, it will properly
handle the dcd's periodicity information (so long as AMBER writes that
correctly -- this is one part I cannot vouch for) and be able to use PME
with pair interactions. I do have one question though -- when you say
you want to get PME periodic interactions, does this mean you /only/
want periodic interactions, or periodic interactions plus those within a
single unit cell? If you mean the former, you'll obviously have to do
one non-periodic, non-pme calculation to subtract the in-cell energy off.

VMD's NAMDEnergy plugin provides a gui for writing namd config files to
do pair interaction calculations, which may be helpful to give you
examples. The bleeding edge version of it also supports PME; let me know
if you're interested in trying that out and I can send you a copy.


Holly Freedman wrote:
> Hi,
> 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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