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

[H.J.Risselada]

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 
>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
> 
> 
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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.
  
gr

Jelger