Re: [AMBER] Energies

From: David A Case <>
Date: Mon, 12 Nov 2018 13:03:25 -0500

On Mon, Nov 12, 2018, Jack Shepherd wrote:
>Is there any way to post process a trajectory in order to analyse e.g. the
>electrostatic energy/force between two nominated residues?

In addition to the imin=5 option in sander, there is also the "energy"
action in cpptraj, which allows you to get energies for parts of the
system via an atom mask.

Remember that the electrostatic energy in a periodic system (computed
via PME) is not pairwise, so you can't directly extract energies between
two groups of atoms. It is possible to learn things by setting the
charges of certain atoms to zero, but you would need to think clearly
about what you are going to do with such calculations.

...good luck....dac

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Received on Mon Nov 12 2018 - 10:30:03 PST
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