MDP condiguration (PKU)

From Bioinformatikpedia

Description of the minimization parameters. See also the gromacs manual.

title = PheOH minimization in vacuum #sets a title; deprecated and ignored option in gromacs 4.6

cpp = /usr/bin/cpp #specifies a c preprocessor; deprecated and ignored option in gromacs 4.6

define = -DFLEXIBLE -DPOSRES #DFLEXIBLE will tell grompp to include flexible water instead of rigid water into your topology, this can be useful for normal mode analysis. 
                             #DPOSRES will tell grompp to include posre.itp into your topology, used for position restraints.

implicit_solvent = GBSA #simulate implicite solvent using the Generalized Born formalism.

integrator = steep #A steepest descent algorithm for energy minimization. The maximum step size is emstep.

emtol = 1.0 #the minimization is converged when the maximum force is smaller than this value.

nsteps = 500 #maximum number of steps to minimize

nstenergy = 1 #frequency to write energies to energy file

energygrps = System #groups to write to energy file, could e.g. be  energygrps = Na Cl Sol to only write solvated ions and solvent

ns_type = grid # Make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps.

coulombtype = cut-off #Twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb≥rlist.
                      #specifies coulomb force calculation, can also be user-specified

rcoulomb = 1.0 #distance for the Coulomb cut-off

rvdw	 = 1.0 #distance for the LJ or Buckingham cut-off (=distance for van-der-Waals forces cut-off)

constraints = none #No constraints except for those defined explicitly in the topology, i.e. bonds and angles are represented by a harmonic (or other) potential.

pbc = no #Use no periodic boundary conditions, ignore the box.