[gmx-users] mdp file

[Sotirios Dionysios I. Papadatos]

Hi,

I am having some trouble defining a proper mdp file for minimization and production runs. I am aware of the manual's - site's reference to this matter, it is pretty thourough.

My question is: How do I know which parameters to use for each simulation? Is there a publication, book etc to guide the user through this? I mean for example if I want to simulate a protein, which parameters do I have to use??