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

[Julian Garrec]

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