[gmx-users] Re: Problem with minimizing the energy of the solvated system
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 5 23:18:35 CEST 2012
On 7/5/12 5:05 PM, jonas87 wrote:
> 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)
You're probably losing the box information somewhere along the line while
switching back and forth between .gro and .pdb. The CRYST1 line in
protein-solvated.pdb should agree with the previous settings. If it doesn't,
something has gone wrong. I recall some previous version of Gromacs had issues
reading and writing correct box vectors in .pdb files; I don't know which one.
It's always safe to use .gro files for everything, though in principle, .pdb
files should work as well.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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