From: Parker de Waal <>
Date: Mon, 16 Mar 2015 22:28:05 +0000

Hi Adrian,

Have you looked into HMR with aMD?


On 3/16/15, 5:40 PM, "Adrian Roitberg" <> wrote:

>Dear all,
>I usually do not like doing this, but I think our recent paper would
>benefit many of you.
>Please take a look at
>"Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning
>Chad W. Hopkins , Scott Le Grand , Ross C Walker , and Adrian E. Roitberg"
>In this paper, we show how to manipulate the masses of atoms in Amber,
>in order to be able to use a time step of 4 fs, while retaining the same
>thermodynamic properties (and essentially the same kinetic properties)
>as you would get when using regular masses and a dt=0.002
>So, you gain a factor of 2x with a very small change.
>If you use Parmed, you can use the HMassRepartitioning command to change
>your prmtop to the 'new' masses, and then just change your mdin to
>Please use it and report back successes and failures !
>Dr. Adrian E. Roitberg
>Department of Chemistry
>University of Florida
>AMBER mailing list

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Received on Mon Mar 16 2015 - 15:30:02 PDT
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