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 <roitberg.ufl.edu>
Sent: Monday, January 23, 2017 5:50:29 AM
To: AMBER Mailing List
Subject: Re: [AMBER] REMD_suggestion
Hi
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
system.
You want to use the SMALLEST value of nstlim that does not make your
simulation (ns/day) slower.
Adrian
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
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=uJw0bDf1BI75KkbFmV7S0JXLmg4xwpQP1JHVPDBWU2g&s=gKdLfCSHmlwYidezxFatsGeKVYXnjF14IDyPkgzHgaI&e=
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=uJw0bDf1BI75KkbFmV7S0JXLmg4xwpQP1JHVPDBWU2g&s=gKdLfCSHmlwYidezxFatsGeKVYXnjF14IDyPkgzHgaI&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 23 2017 - 09:30:02 PST
