Re: [AMBER] REMD_suggestion

From: Thakur, Abhishek <>
Date: Mon, 23 Jan 2017 16:59:45 +0000

Hi Adiran

Thank you so much, I am using implicit water model with dt=0.004.

I will refer to your papers.

Has your group done testing with ntlism which does not slower the (ns/day)? If yes kindly let me know, so that I can start testing my system near to that figure.

From: Adrian Roitberg <>
Sent: Monday, January 23, 2017 5:50:29 AM
To: AMBER Mailing List
Subject: Re: [AMBER] REMD_suggestion


The answer depends a LOT on your setup.

Are you doing this in explicit or implicit solvent ?

My group has a couple of papers out (listed in my web page) where we
show that you should try to exchange as often as you can. Basically,
nstlim should be as small as you can make it. There is a cost associated
with exchanges, so you should benchmark for nstlim=5, 10,100, for your

You want to use the SMALLEST value of nstlim that does not make your
simulation (ns/day) slower.


On 1/23/17 11:46 AM, Thakur, Abhishek wrote:
> Hi everyone,
> I am doing REMD simulation.
> My protein is a dimer and I need a suggestion at what time scale I should allow the exchange?
> I am trying to figure it out but bit confused what can be a goot time step.
> With regards,
> AT
> _______________________________________________
> AMBER mailing list

Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
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Received on Mon Jan 23 2017 - 09:30:02 PST
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