MDP condiguration (PKU)
Revision as of 12:58, 25 June 2012 by Boidolj (Created page with "Description of the minimization parameters. See also [http://www.gromacs.org/Documentation/File_Formats/.mdp_File the gromacs manual]. title = PheOH minimization in vacuum #set…")
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 in stead 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.