[gmx-users] Replica Exchange MD using Gromacs

[Xavier Periole]

Dear Monika,

the setup of a REMD simulation is actually quite straightforward.
In the following I describe steps that would lead you to have a
REMD simulation running on a given system. The "success" of the
simulation will depend entirely on the problem you are addressing
and the criterion you judge it. Although REMD simulation are
helping in increasing sampling they do not provide the ultimate
answer. This should be kept in mind.

Steps:
1) define your system eg: peptide + solvent (implicit or explicit).
2) depending on the amount of processors you can use and the range
of T you want to sample (they are actually extremely dependent on
each other, but you can) you'll have to choose a distribution
of the temperatures. You want to use an exponential distribution:
Ti=T0*exp(k*i) where k and T0 can be tuned to obtain reasonable
temperature intervals to allow exchanges. The exponential allows
an increase of temperature interval as the temperature increases.
This is necessary because the distribution of the total energy
increase with the temperature and thus the exchange rate increases.
You want to keep the exchange rate constant with the temperature.
You can get an idea of the values of T0 and k, by making some
trial ... quite trivial.
3) Once you get your temperature distribution, you use different mdp
files to generate the different tpr files. If you have N temperatures
you should have N tpr files, that you name XXX_0.tpr, ... XXX_N-1.tpr.
4) you can then run short simulations to have an estimate of your
exchange rate (you can get a good estimate within ~100 ps) and
modify the temperatures if it does not correspond to your wished
exchange. Typically 0.2/0.3 is good.
What is actually most important than the value of the exchange rate
itself is the time that a replica will spend at a give temperature.
This is given by the exchange rate*frequency of exchange. eg: an
exchange rate of 0.2 with exchange trials every 2 ps would give you
an average time at a temperature of 10 ps. One point to consider is
also the way you exchange. You may try to exchange all pairs at
each trial or only one pair chosen randomly. In the latter case you
should also take this into account, the residence time of your replica
has then to be multiplied by N-1, the number of pairs you can exchange.
5) the initial conformations at each temperature may be identical or
different. This is your choice and will depend on what you want to
do.

To run the simulation from the XXX_N.tpr files refer to the manual or
earlier emails. I have not used the gmx331/332 versions.

I hope this helps.

Best,
XAvier

> Hi!!
> Thanks for suggestion. But still the problem is that whatever literature
> i have, I could just get the way that they just did replica exchange at
> these or that intervals. But still couldn't get clear the protocol of
> doing replica exchange using Gromacs. That's why i wished for some
> pieces of advice from the experts who have successfully implemented REMD
> using Gromacs.
> Thanks a lot..
> Regards,
> Monika
> On Fri, 2007-11-30 at 14:27 +0200, OZGE ENGIN wrote:
>> Hi Monica,
>> 
>> I had not found a detailed tutorial about it; however, you can search for 
>>papers in which the simulations are performed via REMD.This will be helpful.
>> 
>> Ozge.
>> 
>> -----Original Message-----
>> From: "Monika Sharma" <mon_sharma at research.iiit.ac.in>
>> To: gmx-users at gromacs.org
>> Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST)
>> Subject: [gmx-users] Replica Exchange MD using Gromacs
>> 
>> Dear All,
>> 
>> I am trying REMD for the first time using Gromacs. But I am not finding
>> any much helpful material regarding the replica exchange using Gromacs.
>> Can anyone who has done REMD please let me know about any good tutorial
>> where I can understand the way this replica exchange work in gromacs and
>> the right protocol to do so..
>> 
>> Thanks a lot in advance..
>> 
>> Regards,
>> Monika
>> CCNSB, IIIT,
>> Hyderabad.
>> 
>> 
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> 
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------