[gmx-users] stochastic dynamics , langevin
omermar at gmail.com
Thu Oct 23 15:31:16 CEST 2008
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 (
Your help is appreciated. Omer.
Koby Levy research group,
Weizmann Institute of Science.
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