Re: NAMD energy run in VMD

From: Peter Freddolino (
Date: Tue Nov 21 2017 - 13:02:07 CST

Dear Srjita,

On Nov 21, 2017 10:46 AM, "Srijita Paul" <> wrote:

I have some doubts in namd energy calculation from vmd.
1.If I want to calculate intermolecular interaction energy between same
molecule what will be the sel1 and sel2 selection. Because same name in
sel1 and sel2 does not work.

Quoting the namdenergy documentation:
The argument for the -sel switches is a variable containing either one or
two atom selections; if a single selection is given (*i.e.*, -sel $sel1),
then energies for that selection are calculated. If two selections are
given (-sel $sel1 $sel2), only interactions between the two selections will
be calculated

2.For generating xsc file what will be the input in x-length and centre .Is
it final box length and half box length of the system respectively?

Are you running on a single snapshot or a trajectory?

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