I would also add that you could also use TEE-REX which overcomes some of
the problems associated with normal REMD on large systems. Do note that as
far as i know the TEE-REX patch only works with GROMACS versions 3.3.x and
so each replica in the TEE-REX simulation can only be ran on one CPU,
meaning that these simulations can take a long time.
Tom
--On Friday, November 20, 2009 16:11:38 +0100 Berk Hess <g...@hotmail.com>
wrote:
Hi,
I would think any system with a membrane in it is too large to gain much
with REMD
(unless you are interested in the temperature dependence).
You can use essential dynamics sampling or flooding, see make_edi.
Berk
Date: Fri, 20 Nov 2009 10:00:11 -0500
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Pushing MD further
Thielges, Sabine wrote:
> Hi,
>
> I am currently running some GPRC MD with membrane. After a lot of trial
> I now have a nice 25 ns run with an agonist. But the final structure is
> too close the starting and I know it is far from what the biology
> describes.
> I would like to know if there is options that I can add to my md.mdp
> file to make the MD "explores some other area".
>
There is no magic .mdp option to make sampling better, and you can not
necessarily ever trust the results of just one single simulation. There
are several options to enhance sampling:
1. Simulated annealing
2. Replica-exchange MD
3. Additional simulations with different starting velocities
With #2, bilayers can be quite problematic. A recent paper from Max
Berkowitz's group in JPCB has a nice protocol for REMD with a membrane.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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