[gmx-users] Locally Enhanced Sampling

[msonoda at iqm.unicamp.br]

> msonoda at iqm.unicamp.br wrote:
>>> Ran Friedman wrote:
>>>> Hi,
>>>>
>>>> You're probably better off with moil.
>>>>
>>> That does seem to have it implemented.
>>>
>>> Naive question: what does the algorithm do?
>>
>>
>> Locally Enhance Sampling was initially
>> proposed by Elber and Karplus
>> (jacs, (1990) 112:9161) to study
>> carbon monoxide escaping through
>> myoglobin. To improve sampling,
>> many copies of a small part of
>> the system (eg CO) are made,
>> where the copies DO NOT interact
>> each other, the interaction between
>> the copies and the large part
>> of the system (eg myoglobin)
>> is scaled by the number of copies.
>> In this way, the energy barrier
>> that CO must overcome to scape is
>> decreased, and the probability of
>> observation of a scape is increased
>> exponentially.
>>
>> Many theoretical improvements in the
>> method has been done by Ulitsky, Elber,
>> Straub and Karplus
>> (JCP (1993) 98:3380; JCP (1991) 94:6737;
>> JPC (1994) 98:1034).
>> Basically, they wanted to map the
>> dynamics of each copy to the dynamics
>> observed if there were not copies
>> (ie one single CO) in order to observe
>> correct time dependent properties.
>
> OK, so what happens if I diminish the interactions by a factor of 50 and
> put in 50 copies of the CO molecule?
>
> Is that enough? Or is there some kind of funky coupling?
>
>

To my knowledge, this was done in the first paper
(Elber and Karplus, jacs, (1990) 112:9161).
But this aproach has the problem that the kinetic
energy encreases with the number of copies.
I'm not sure but the improvement of the method involve
reducing the mass of the copies to make kinetic energy
constant. However this introduces another problem:
the difusion of the copies is artifactually
encreased. To avoid this they also make an group
termalization.

>>
>>
>>>> Ran.
>>>>
>>>> Alexandre Suman de Araujo wrote:
>>>>
>>>>> Hi Gmxers!
>>>>>
>>>>> I´d like to perform some Locally Enhanced Sampling (LES) simulations
>>>>> of a ligand in a protein and I´d like to know if it´s possible with
>>>>> Gromacs and, if yes, what I need to do to implement this kind of
>>>>> simulations.
>>>>> Thanks!
>>>>>
>>>>
>>>
>>> --
>>> David.
>>> ________________________________________________________________________
>>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
>>> phone:	46 18 471 4205		fax: 46 18 511 755
>>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>
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>>
>>
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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