From: John Stone (
Date: Tue Dec 08 2015 - 14:06:14 CST

There isn't a pre-written script to do what you ask included in VMD,
but I'm sure you could write one. I assume that you're using NAMDEnergy
for your energy evaluation? Keep in mind that any calculation involving all
pairs has quadratic runtime and will be very slow for anything other than
a very small system, as well as generating a lot of output.

  John Stone

On Tue, Dec 08, 2015 at 11:48:04AM +0300, elena ermakova wrote:
> Hello,
> I would really appreciate if anyone can provide some input to the
> following question:
> VMD is able to calculate interaction energy between any pair of residues
> along the trajectory.
> Question is:
> Is any script which allow to calculate the interaction energies between
> ALL pairs of residues ( may be in cycle) and save them to file or files?
> Thank you very much.
> Elena

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