[gmx-users] Pushing MD further

[TJ Piggot]

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 <gmx3 at 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: jalemkul at vt.edu
>> To: gmx-users at 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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>
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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.