[AMBER] On the skipping of first frames in mmpbsa calculations

From: Enrico Martinez via AMBER <amber.ambermd.org>
Date: Mon, 12 Sep 2022 14:25:53 +0200

Dear Amber users!
I have a question related to the mmpbsa calculations of free energies
of binding.
In the literature I saw that commonly several first frames of the
trajectory should be omitted from the computing.

I've just done a quick test with 150 ns trajectory, omitting i) the
first 25 and then ii) the first 50 ns and could see a difference in 10
kkal/mol for the complex with moderate predicted values. How could I
select a proper strategy for this ?
Many thanks in advance

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Received on Mon Sep 12 2022 - 05:30:03 PDT
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