[gmx-users] Re: Can I run BD in water media using Gmx?(H.J.Risselada)

[Hu Zhongqiao]

Thanks, Mark and Jelger,

To Jelger, 

But If one can run BD by setting integrator=sd, how is dielectri
constant of water set in the simulation? On p141 of the Manual v3.3,
there is one option epsilon_r. Does it mean BD can be run successfully
if epsilon_r is set as ca. 78 for water? 

zhongqiao


> GROMACS does not permit implicit solvent models for any 
>of its integration methods. Other simulation packages do.
> 
> Mark
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If I am not mistaken implicit solvent is implemented in 
GMX  for using sd integration. (Never did any proteins ;), 
so don't blame me if I'm wrong.)

The GB82 langevin integrator implemented in gromacs 
(option "sd" in mdp file) is however a generalized 
langevin integrator. The BD euler scheme (bd in mdp file), 
is just a solution of the same differential equation as 
the SD equation, however now this differential equation 
can be simplified as some terms (inertia) become 
insignificant in the limit of high friction.

"Generalized" means that the sd-scheme in gromacs is 
capable to solve the equations of motions in both the 
newtonian limit (tau_t >>> 0) as well as in the brownian 
regime (tau_t -> 0 ).
Ofcourse, it can still only handle the friction 
coefficients in the limits to some numerical extend. If 
the friction coefficent is reasonable small you will be 
still able to do brownian dynamics with the sd integrator 
and use implicit solvent options.

Anyway,

Good luck !!!!!!!

greetings

Jelger