[gmx-users] Locally Enhanced Sampling
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 16 13:40:10 CET 2006
msonoda at iqm.unicamp.br wrote:
>> Ran Friedman wrote:
>>> 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
> 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?
>>> 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
>> 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
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users