[gmx-users] Locally Enhanced Sampling

[msonoda at iqm.unicamp.br]

> 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.


>
>> 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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