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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, July 25, 2020 8:36:21 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] How to install Amber20 with pmemd.amoeba?
On Sat, Jul 25, 2020, Kliuchnikov, Evgenii wrote:
>
>I am trying to perform MD simulations in Amber20 with AMOEBA force
>field. I believe that for that purpose I am supposed to use pmemd.amoeba,
>but I can not find it installed. I used gem.pmemd instead which is also
>allows me to perform AMOEBA calculations, but it is too slow. I did not
>find any clear description of how to install pmemd.amoeba.
We have not distributed pmemd.amoeba in a long time. The gem.pmemd code,
a successor to pmemd.amoeba, is the only part of Amber that carries out
calculations with the amoeba force field. This code is primarily aimed at
the "GEM" forcefield, but also supports AMOEBA, which is subset of GEM.
Those requiring faster AMOEBA codes might want to look at Tinker, and its
partnership with OpenMM: so far as I know, that is the only GPU-enabled code
that supports AMOEBA.
....dac
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Received on Sat Jul 25 2020 - 22:00:03 PDT
