Hi,
I ran minim.mdp for my system with 3456 atoms. But lowest energy after
minimization is positive.
*here is th screen output*
Step= 4509, Dmax= 4.5e-05 nm, Epot= 4.06554e+02 Fmax= 9.86206e+00, atom=
3521
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to Fmax < 10 in 4510 steps
Potential Energy = 4.0655389e+02
Maximum force = 9.8620596e+00 on atom 352
Norm of force = 3.3500545e+00
NOTE: 16 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
*Below is txt of minim.mdp file *
; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emstep = 0.01 ; Energy step size
;emtol = 1000.0 ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
nsteps = 500000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 10 ; Frequency to update the neighbor
list and long range forces
rlist = 2 ; cut-off for making neighbour list (short
range forces)
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list
(simple, grid)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rcoulomb = 0.9 ; Short-range electrostatic cut-off
rvdw = 0.9 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
regards
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