title=polylys_min ; This gives a title for the run
cpp=cpp ; This tells grompp the name of a “C-preprocessing” (cpp) program that it can use to interpret the .top file. This program is just called cpp on the workstation.
integrator=steep ; This tells GROMACS to run a steepest descents minimization.
nsteps=1000 ; This tells GROMACS the maximum number of steps to perform. If the minimization doesn’t converge within this number of steps the run will end anyway.
nstlog=10 ; This tells GROMACS how frequently to save information to the .log file, which provides a summary of the run.
nstenergy=5 ; This tells GROMACS how frequently to save energies to the
energy output (.edr) file.
xtc_grps=Protein ; This tells GROMACS which parts of the simulation system to put in a trajectory file (.xtc) that saves the coordinates during the minimization. Here, there’s only a protein (e.g. no water or other molecules), so this is pretty obvious.
energygrps=Protein ; This tells GROMACS which parts of the simulation system to put in a the energy output file (.edr) that saves the system energies during the minimization. Again, there’s only a protein here.
rlist=1.0 ; This tells GROMACS the cutoff distance (in nm) for calculating the “neighbor list” of atom pairs that need to have non-bonded interactions calculated. If this is different than the next two, it specifies a “twin-range” cutoff, where some longer range interactions (pairs > rlist but < rcoulomb or rvdw) aren’t calculated every single step.
rcoulomb=1.0 ; This tells GROMACS the cutoff distance (in nm) for calculating coulombic interactions
rvdw=1.0 ; This tells GROMACS the cutoff distance (in nm) for calculating van der Waals interactions
This is an energy minimization mdp. Maybe something like this might work (I will comment the lines that are not used anymore)
; title = polylys_min ; drop this
; cpp=cpp ; not used, you use directly gmx grompp to compile now
integrator = steep ; here is EM, okay
nsteps = 1000 ; very short, I would go for 50k or so
nstlog = 10 ; ok as is but very short, would just drop this line and keep the default (1000)
nstenergy = 5 ; ok as is but very short, would just drop this line and keep the default (1000)
; xtc_grps = Protein ; this is called now compressed-x-grps, so it becomes
compressed-x-grps = Protein; print only the protein in the xtc file
energygrps = Protein ; ok
rlist = 1.0 ; ok, it's the default
rcoulomb = 1.0 ; ok
rvdw=1.0 ; ok
As a side note, if the systems consists only of a protein in vacuum then the lines compressed-x-grps = Protein and energygrps = Protein are useless as the whole system is just the protein so this is equivalent to drop these lines and print the default (System). Also I would in general just drop these lines and keep all the output all the time, and I would also drop and the nstlog and nstenergy lines and keep the defaults (1000) but here it’s up to you, as I do not know if you need this much output.
Thank you for your attention and support.