AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 16 2008 - 09:45:38 CDT

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
<http://www.ambermd.org/tutorials/advanced/tutorial7/files/remd_chem_phys_le
tt.pdf> (
<http://www.ambermd.org/tutorials/advanced/tutorial7/files/remd_chem_phys_le
tt.pdf> "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

 

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