All possible *.mdp file paramters are described in the mdp options sections of the
Gromacs Online Reference.
It would be ideal to open it in a separate browser tab while walking through the file.
ions.mdp
; Neighbor searching
cutoff-scheme = Verlet
rlist = 1.1
pbc = xyz
verlet-buffer-tolerance = -1
; Electrostatics
coulombtype = PME
pme-order = 4
fourierspacing = 0.10
rcoulomb = 1.0
; VdW
rvdw = 1.0
continuation = yes
The cutoff-scheme sets the algorithm that is used to detect neighbors of each particle.
The Verlet scheme is a very efficient and scalable method that keeps a list (a buffer) of close particles
and searches only those to detect neighbors within a given cutoff.
The cutoff value can be fixed with the rlist option or set indirectly by specifying
a maximally allowed error with verlet-buffer-tolerance
(verlet-buffer-drift in Gromacs 4).
The pbc option switches on periodic boundary conditions.
Next we specify that the algorithm used for computing long range electrostatic interactions should be
Particle-Mesh-Ewald (PME) and set some parameters.
A cutoff value up to which VdW interactions are taken into account is also specified.