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. http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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