AMBER Archive (2008)

Subject: Re: AMBER: Plea for REMD tutorial

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Feb 29 2008 - 11:47:47 CST

have you looked at the examples in the test directory?
it might help if you're specific about which part of REMD
is giving you trouble. REMD in Amber is intended to be an
advanced topic and it assumes you are already very comfortable
with regular MD and have also read the REMD literature to
see how it is usually done. We are finishing a tutorial but it
will explain only technical things and not choices that must be
made, such as # of replicas and their temperature distribution,
which you can find discussed in the literature. If you know how REMD
works then we can certainly help you to understand the options
that make it work in Amber.

On Fri, Feb 29, 2008 at 9:57 AM, tushar garud <tushar.garud07_at_gmail.com>
wrote:

> Hello sir,
> I am doing a project in conformational sampling of an oligopeptide using
> REMD in a academic carrier. I am using amber 9 version. I am going to do
> it for four replicas. Can you please provide a sample protocol for
> Replica-exchange molecular dynamics method of an oligopeptide?
>
> Thanking you,
>
> Tushar Garud.
>

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