[gmx-users] query regarding type of MD for protein protein interaction
drrahulsuresh at gmail.com
Tue Apr 2 08:15:54 CEST 2019
On Tue 2 Apr, 2019, 11:34 AM p t, <parulscholar at gmail.com> wrote:
> Hello All,
> this is not a working problem in gromacs, but rather a starting problem i
> am facing.
> I have to study GPCR oligomerization and will do the simulation in a lipid
> bilayer environment, and later also find kinetic rates through simulation.
> I read a lot of papers, some suggest Replica exchange method for studying
> the Pr-pr interaction and some metadynamics.
> though some studies also suggest Coarse grained but i think it will not be
> so beneficial as i need to predict kinetics later and lot of information
> will be lost in coarse grained.
> one of the criteria for selection is less time to be taken for these
The simulation cost not only depends on the method but also on the system.
The option of right method depends on your exact aim of the work.
> I dont want to start the work and realize that other method could have been
> better, a valuable input would be highly appreciated.
This is true because, gpcr simulation and especially oligomerization is
> thank you
Personally I suggest REMD, though I haven't worked on it, I find remd
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