AMBER Archive (2009)

Subject: Re: [AMBER] REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 23 2009 - 05:07:39 CDT

there is really nothing special about REMD in this regard. systems that work
in MD will work in REMD. you don't need to neutralize the charge just as you
don't for MD, but there might be reasons why you would want to do it (the
same as for MD).
keep in mind that remd on large proteins is not well studied- if you don't
have a lot of experience, make sure you are reading the literature and
following what other have done.

On Tue, Jun 23, 2009 at 1:32 AM, Shaikh Abdul R S Ramaju <
smasarsr_at_nus.edu.sg> wrote:

> Dear Amber Users,
>
>
>
> I am trying to use the Replica exchange molecular dynamics for the
> protein molecule. Total charge on the system is -3.00. Do I need to
> neutralize the charge before creating topology file or I can use it as
> such?
>
>
>
> Thanks a lot
>
>
>
> Regards
>
> Abdul Rajjak
>
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