[gmx-users] langevin dynamics and manual

Marius Retegan marius.s.retegan at gmail.com
Tue Feb 3 19:07:55 CET 2009


I have a comment regarding the Gromacs manual. For equation (3.62) in
Chapter 3.8, \epsilon_i is called the friction constant. This is incorrect
since in that equation \epsilon is actually collision frequency and should
be represented with the letter \gamma. The product of the collision
frequency with the atomic mass gives the friction constant (\zeta). It will
also be helpful to add to description of the mdp options for Langevin
dynamics the fact that for bd_fric=0, \zeta = m / tau_t, where tau_t is the
inverse of the collision frequency \gamma. I say all this since in other
packages you define \gamma directly and not its inverse, and this can cause

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