[gmx-users] Basic GROMACS questions

Simone Bolognini simo.bolognini at gmail.com
Mon Dec 8 10:47:38 CET 2014

I started using GROMACS like 2-3 weeks ago and I'm doing the first steps in
the comprehension of the subject (I'm a physicist, but not skilled in
molecular dynamics). Therefore, I have some basic questions to ask to you:
1) are there any conceptual problems in using different running parameters
for "in solvent" energy minimization, position restrained dynamics and
dynamics? For example: would it lead to some "absurd results" if I use
Berendsen pressure and temperature coupling for position restrained
dynamics and Nose-Hoover and Parrinello-Rahman for the actual dynamics?
2) which is the most reliable force field for GROMACS 4.5.6? For all my
simulations I always used the last version of the Gromos ones: would you
suggest something different?
3) for the dynamics of a protein, would you use PME electrostatics or
Reaction-Field one? Again: is there any conceptual problem in using
different electrostatics parameters in the different stages of simulation?
I would guess there are, but in the various tutorials I saw it seems that
many people change settings "on the run".
4) in a perfect world, where running time is not a problem, what kind of
.mdp file would you set for the dynamics of a small protein? I mean: is
there a general recipe to do things correctly (and in a realistic fashion)
or is it really case dependent?

Thank tou very much for your answers!

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