AMBER Archive (2007)

Subject: Re: AMBER: replica exchange

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Oct 28 2007 - 10:38:15 CST

no, there is no practical way to combine multisander and pmemd.
you can run REMD with pmemd using scripts, although I have
not done this myself so I cannot provide examples.
you can certainly "compile amber from scratch", but I'm not
sure what yuo're getting at. It certainly won't scale as well in cpus
per replica as pmemd does.

On 10/28/07, Geoff Wood <geoffrey.wood_at_epfl.ch> wrote:
> Dear Amber users,
>
> I am interested in utilizing a Blugene/L machine that I have available to
> me. I successfully compiled and ran PMEMD calculations on the BG/L using
> the config files available from the following link
> http://amber.scripps.edu/config.bgl.html however, I have
> just realised that remd is not implement in PMEMD. Is there a way of
> including the routines in multisander in the PMEMD compilation or compiling
> sander from scratch using similar config files? I don't think sander will
> have scaling problems on a BG/L when using remd because although you could
> utilize many cpus it is the number of cpus per replica that counts.
>
>
> Kind regards
>
>
> Dr Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
>
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