[gmx-users] query regarding type of MD for protein protein interaction

RAHUL SURESH 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
> simulations.
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
highly expensive.

> thank you
> parul

Personally I suggest REMD, though I haven't worked on it, I find remd
really helpful.

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