[gmx-users] Re: Can I run BD in water media using Gmx? (Hu Zhongqiao)
H.J.Risselada at rug.nl
Wed Jan 10 15:33:10 CET 2007
On Wed, 10 Jan 2007 17:36:10 +1100
Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Hu Zhongqiao wrote:
>> Nobody implied me till now. So that means the current
>>version can not do
>> BD by implicitly treating water into continuum media,
>>i.e, use of
>> dielectric constant of water. I hope Gmx developers can
>>help me to make
>> sure this. Till to now I am been using Gmx and in the
>>near future I need
>> to do BD for longer time scale. If Gmx can not help, it
>>will be bad.
> 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 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.
Good luck !!!!!!!
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