[gmx-users] Pushing MD further

[mkubitz at gwdg.de]

There exists a (non-official) TEE-REX prototype for GMX 4 which allows
full parallelization of each TEE-REX copy. Just contact ckutzne at gwdg.de
for more information.

Marcus


> 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.
>
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