annotate test-data/minim.mdp @ 6:6dcfdac2dcae draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit ab7232ec03a3361f808f5a0be0828e0f7fbd376d"

; minim.mdp - used as input into grompp to generate em.tpr
integrator  = steep    ; Algorithm (steep = steepest descent minimization)
emtol    = 1000.0     ; Stop minimization when the maximum force is less than this value
emstep      = 0.01      ; Energy step size
nsteps    = 50000      ; 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
cutoff-scheme   = Verlet
ns_type        = grid    ; Method to determine neighbor list (simple, grid)
coulombtype      = PME    ; Treatment of long range electrostatic interactions
rcoulomb      = 1.0    ; Short-range electrostatic cut-off
rlist       = 1.0 ; Cut-off distance for the short-range neighbor list.
rvdw        = 1.0    ; Short-range Van der Waals cut-off
pbc            = xyz     ; Periodic Boundary Conditions (yes/no)