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

From: Hosein Geraili Daronkola <geraili.hsn.gmail.com>
Date: Mon, 10 May 2021 00:15:01 +0200

Dear all,

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. This issue is exacerbated when I use soft-core
potential for charged species, one-step transformation. If this is from the
end-point singularity, it might mean that the TI integration renders a
finite result, although single MBAR energies show that (I am using
soft-core potential!!). But without using soft-core potential, I don't get
the correct result for linear scaling of removing the charge.

Has anybody encountered the same problem? What could be the reason
behind this?

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Received on Sun May 09 2021 - 15:30:02 PDT
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