I’m very, very new to the use of GROMACS and the world of computational simulation. But, one question came to me: when we define an mdp file for a minimization, for example, the gmx grompp makes another mdp file with all the parameters. Do these values make any difference in the process?
The mdout.mdp file generated by grompp contain all the parameters that were actually used, so they do make a difference in the process. Everything that was not specified in your input mdp was filled in with default values.
Is it safe to trust the default values? For most parameters, the defaults is equal to “feature disabled”, hence unimportant. However, there are certain parameters where the chosen value is important for the accuracy of the simulation, and the default might not be correct, like constraints, vdwtype, rvdw, vdw-modifier, rcoulomb, DispCorr. These should be set according to the recommendation of the creator of the force field used, as you will want to simulate under the same conditions the force field was calibrated under.