[gmx-users] Re: Problem with minimizing the energy of the solvated system

[jonas87]

I'm following the tutorial exactly. Even have my files named the same way.
The contents of my minil.mdp (pcb is changed from no to xyz right before
running the energy minimazation of the solvated system):

title		= Energy Minimization	; Title of run
cpp		= /lib/cpp	; Preprocessor
define          = -DFLEXIBLE
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1.0		; Stop minimization when the maximum force < 1.0 kJ/mol
nsteps		= 500		; Maximum number of (minimization) steps to perform
nstenergy	= 1		; Write energies to disk every nstenergy steps
energygrps	= System	; Which energy group(s) to write to disk
ns_type		= simple	; Method to determine neighbor list (simple, grid)
coulombtype	= cut-off	; Treatment of long range electrostatic interactions
rcoulomb	= 1.0		; long range electrostatic cut-off
rvdw		= 1.0		; long range Van der Waals cut-off
constraints	= none		; Bond types to replace by constraints
pbc		= no		; Periodic Boundary Conditions (yes/no)



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