Re: [AMBER] How to compute pairwise interaction between masks

From: Dr. Anselm Horn <>
Date: Mon, 13 Sep 2021 11:11:46 +0200

Dear Mathew,

maybe the cpptraj-command lie (linear interaction energy) does what you
want (see p. 703, section 34.11.41 Amber21 manual).
With lie you can compute the electrostatic and vdW interaction energy
between two groups of atoms defined by Amber masks. The calculation is
done in cpptraj and is very fast.

Alternatively, you maybe could use the cpptra-command energy (see p.
689, section 34.11.30 Amber21 manual) to compute the interaction energy
of your two sets of atoms by hand.

While I haven't used the energy command so far, I have successfully
applied the lie feature to compute interaction energies between groups
of atoms within a system over the course of a trajectory.



On 09/10/2021 11:26 PM, Matthew Guberman-Pfeffer wrote:
> Dear Amber Community,
> I want to compute the interaction energy between two masks, not for the atoms within a given mask (i.e. something akin to the PairInteraction feature of NAMD). Is there a way to do this in CPPTRAJ? I’ve looked at the pairwise function, but that feature doesn’t seem to compute the energy between two masks.
> Best,
> Matthew
> _______________________________________________
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Received on Mon Sep 13 2021 - 02:30:02 PDT
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