Module 4 : Classical Molecular Dynamics using Gromacs
Chapter 33 : Molecular dynamics simulation of water
 
33.7 Energy minimization of initial configuration:

The energy of system can be minimized with the help of em.mdp file. The em.mdp file is given below.
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; em.mdp - used as input into grompp to generate em.tpr file

; Parameters describing what to do, when to stop and what to save are given below.
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0    ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01     ; Energy step size
nsteps = 5000     ; Maximum number of (minimization) steps to perform
 

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1         ; Frequency to update the neighbor list and long range forces
ns_type = grid      ; Method to determine neighbor list (simple, grid)
rlist = 1.0       ; Cut-off for making neighbor list (short range forces)
coulombtype = PME       ; Treatment of long range electrostatic interactions
rcoulomb = 1.0       ; Short-range electrostatic cut-off
rvdw = 1.5       ; Short-range Van der Waals cut-off
pbc = xyz       ; Periodic Boundary Conditions
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