Hi,
I had sent over a zip with files some time ago but I now noticed that I can only send tiny file sizes, and that the message was likely never delivered. I have instead hosted the files on guthub at
https://github.com/gundelach/AmberMailingListQuestion
It contains two identical trajectories of 2 frames each, one autoimaged and rms fit, the other without. Produce different energies.
Best wishes,
Lennart
From: David A Case <david.case.rutgers.edu>
Date: Wednesday, 12 May 2021 at 15:01
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame
CAUTION: This e-mail originated outside the University of Southampton.
On Wed, May 12, 2021, Lennart Gundelach wrote:
>
>This was because the MMPBSA.py 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
>approach).
>
>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....
....dac
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Received on Thu May 27 2021 - 02:30:02 PDT
