[gmx-users] Re: Can I run BD in water media using Gmx? (H.J.Risselada)
H.J.Risselada at rug.nl
Thu Jan 11 03:35:05 CET 2007
On Thu, 11 Jan 2007 09:50:12 +0800
"Hu Zhongqiao" <zhongqiao_hu at nus.edu.sg> wrote:
> Thanks, Mark and Jelger,
> To Jelger,
> But If one can run BD by setting integrator=sd, how is
> constant of water set in the simulation? On p141 of the
> there is one option epsilon_r. Does it mean BD can be
> if epsilon_r is set as ca. 78 for water?
>> GROMACS does not permit implicit solvent models for any
>>of its integration methods. Other simulation packages do.
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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
> 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
> and use implicit solvent options.
> Good luck !!!!!!!
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For specific questions, my former collegue Fan Hao was
doing implicit solvent simulation in gromacs using
non-public available code.
I initialy thought it allready had been standardized in
gromacs.....but probably not... (why not ?). I will send
you his email adress.
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