Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI

From: David A Case <>
Date: Mon, 10 May 2021 09:00:31 -0400

On Mon, May 10, 2021, Hosein Geraili Daronkola wrote:
>When I use soft-core potential for TI, in GPU pmemd 2018, for many of the
>intermediate states I get MBAR energies for either lambda 0 or 1, which is
>either very different from the other lambdas, sometimes very positive, and
>sometimes "**********". If I just ignore this issue my result looks fine
>with TI calculations.

There were bugs in the MBAR printouts in Amber18, but I don't know much
about the details. Maybe Ray Luo or Charlie Lin will recognize the symptom,
or have a different suggestion.

It's probably worth upgrading to Amber20 (and apply all the updates).
Or, you might try applying Amber20, update.7 to your 2018 code, either by
hand or by using patch. It only involves a one-line change in
mdin_ctrl_dat.F90. Of course, you problem might have some other origin.


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Received on Mon May 10 2021 - 06:30:02 PDT
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