AMBER Archive (2008)

Subject: Re: AMBER:Some questions about replica exchan ge

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 16 2008 - 10:04:25 CDT

you might look at the discussion of spacing and some of the references
given in this paper:
Cheng, X., Cui, G., Hornak, V. and Simmerling, C., "Modified Replica
Exchange Simulation Methods for Local Structure Refinement". J. Phys.
Chem. B, 109, 8220-8230 2005

On Wed, Jul 16, 2008 at 10:45 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Zehan,
>
>
>
> I would suggest you first work through the REMD tutorial to get a sense of
> how to run such a simulation.
> http://www.ambermd.org/tutorials/advanced/tutorial7/index.htm
>
>
>
> Then I suggest you start by reading some of the literature on Replica
> Exchange to make sure you understand it. This way you will learn how others
> have selected replica counts and temperature distributions and understand
> why they did it that way.
>
>
>
> I suggest starting with the Sugita and Okamoto paper on REMD:
>
>
>
> Sugita and Okamoto ("Replica-exchange molecular dynamics method for protein
> folding." Chemical Physics Letters 314(1-2): 141-151, 1999)
>
>
>
> I would then look at some of the papers that have cited this and read those
> as well. Do not start blindly running REMD simulations without at least some
> knowledge of the literature and an understanding of what these simulations
> actually are.
>
>
>
> Good luck,
>
> Ross
>
>
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> huzehan19870731_at_126.com
> Sent: Wednesday, July 16, 2008 6:08 AM
> To: amber_at_scripps.edu
> Subject: AMBER:Some questions about replica exchan ge
>
>
>
> Dear all,
>
> I want to perform MD simulations using replica exchange method. However,
> before starting the replica exchange simulation, I need to determine the
> number of replicas and the temperatures for each replica for the simulated
> system.
>
> I have no idea how to choose these, i.e. the reasonable numbers of replicas
> to use and an optimum temperature distribution.
>
> Can someone give me some advices, and any command of yours will be a great
> help for me.
>
> Thank you.
>
> Sincerely,
>
> zehan hu
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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