Re: [AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI

From: Daniel Roe <>
Date: Fri, 8 Feb 2019 10:30:59 -0500


> I am scaling my system on a temperature ladder, and to allow an potential energy overlap between so few replicas, I am using an Hamiltonian scaling on the water molecules, 'to cool them down' (solute tempered method, REST1), I then obtain a flatter and lower energy distribution for 'hotter' replicas, where I only warm up the protein.

It's unclear to me how you are doing this with Amber. As far as I know
REST-type methods are not supported by Amber. Could you provide more
details on what you are doing here (input files, code modifications,

> My hypothesis is that this behavior comes from the rule to calculate probability

One thing you could do to test this is to run the simulations but do
not exchange, i.e. set numexchg to 1 and nstlim to whatever
numexchg*nstlim was previously. If the problem is with the exchange
calculation this should eliminate the issue.


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Received on Fri Feb 08 2019 - 08:00:04 PST
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