[gmx-users] stochastic dynamics , langevin

Omer Markovitch omermar at gmail.com
Thu Oct 23 15:31:16 CEST 2008

Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins.
After reading the manual & going over some old mails in this list, I have
two points I hope you could clear for me:
[Gromacs version 3.3.3]

1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
proper keywords I should use for Langevin dynamics:
integrator = sd ;
bd-fric    = 0 ;
tau_t      = 10 ;
ref_t      = 300 ;
With bd-fric=0, the friction is taken as the inverse tau_t.

2) From your experience, what are good values of tau_t (or 1/tau_t) for
simulating a protein? In 2006 list, David has commented that choosing tau_t
is very important (
http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).

Your help is appreciated. Omer.

Koby Levy research group,
Weizmann Institute of Science.
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