[gmx-users] Langevin thermostat implementation in GROMACS vs AMBER

[Julian Garrec]

No suggestion ?? :)

In my post I forgot to say that my system contains explicit water.

I'm still very curious about the difference in implementation in AMBER 
and GROMACS. And I still don't really understand the meanning of tau-t 
in LD and how  it is related to other (well defined) quantities such as 
the friction coeficient in equation 3.114 of the manual (v4.6.1).

Please help,

Sincerely,

Julian


Le 04/05/13 13:42, Julian Garrec a écrit :
> Dear all,
>
> I am trying to use stochastic dynamics in GROMACS to reproduce some 
> previous results that I got with the AMBER software using the Langevin 
> thermostat.
>
> In AMBER, one typically sets what they call the "collision frequency" 
> (noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2 
> collisions per ps (significantly smaller than the internal friction of 
> water, since I use Langevin dynamics as a thermostat).
>
> 1) In the mdp options manual, it is recommended to use {integrator=sd 
> ; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds 
> to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the 
> manual (version 4.6.1). Am I right ?
>
> 2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to 
> {integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the 
> manual, it is said that gamma_i should be set to 0.5 to follow the 
> same spirit).
>
> 3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
>
> Thanks for your help,
>
> Julian
>


-- 
Julian Garrec, research associate

Web: https://sites.google.com/site/juliangarrec/

Équipe : Chimie et Biochimie Théoriques
Unité Mixte de Recherches CNRS UHP 7565
Université de Lorraine, Nancy I BP 239,
54506 Vandoeuvre-lès-Nancy, cedex France