Re: [AMBER] and rms fit: Results depend on reference frame

From: David A Case <>
Date: Wed, 12 May 2021 09:00:55 -0400

On Wed, May 12, 2021, Lennart Gundelach wrote:
>This was because the script does
>an autoimage and rms fit on the whole trajectory before calculation
>energies or entropies (which it obviously cant in the snapshot by snapshot
>I have naively been assuming, that the energies obtained would be invariant
>under rotations and translations of the system and that the final energies
>would not depend on the choice or reference frame or ordering of the
>trajectory. This is not the case.

>My fix is simply to autoimage and rms fit the trajectory before slicing it
>into individual snapshots,

Can you find a snapshot that gives a different energy before the
autoimage/rms and afterwards? I think that will be needed to figure out
what is going on. [Since MMPBSA is interpreting part of a periodic snapshot
in a non-periodic fashion, it's certainly possible that autoimage might not
be doing the desired thing here: autoimage is coded for periodic systems.]

As an aside, I don't (immediately) see how you are going to average energies
that arise from snapshots with different numbers of waters. But I haven't
given that a lot of thought....


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Received on Wed May 12 2021 - 06:30:03 PDT
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