Re: [AMBER] MBAR from TI on pmemd

From: <>
Date: Fri, 22 Feb 2019 09:25:23 -0500

Hi Hosein,

        Prof. Mobley has a python code to do so:

        In TI, there is no such thing really defined as "overlapping"--and
TI results do not depend on overlaps between windows. The critical thing
for TI is that the du/dl curvature is smooth enough for decent numerical

        Anyway, Prof. Mobley's tool utilizes the pymbar library, which can
generate overlapping results for MBAR.


-----Original Message-----
From: Hosein Geraili Daronkola <>
Sent: Friday, February 22, 2019 5:34 AM
To: AMBER Mailing List <>
Subject: [AMBER] MBAR from TI on pmemd

I am running TI with Amber18 using Soft Core.
I wanted to know how can I use the MBAR data in my output to use MBAR
calculation??? I mean, is there any script in AmberTools to do that, or
outside AmberTools?? What criteria would people normally use to validate
that the overlapping of the potential between two consecutive lambdas is
sufficient for AMBER TI calculation??


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