Difference between revisions of "MDP condiguration (PKU)"

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(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…")
 
 
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title = PheOH minimization in vacuum #sets a title; deprecated and ignored option in gromacs 4.6
 
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
 
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.
 
  +
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.
 
#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.
 
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.
 
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.
 
emtol = 1.0 #the minimization is converged when the maximum force is smaller than this value.
  +
 
nsteps = 500 #maximum number of steps to minimize
 
nsteps = 500 #maximum number of steps to minimize
  +
 
nstenergy = 1 #frequency to write energies to energy file
 
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
 
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.
 
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.
 
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
 
#specifies coulomb force calculation, can also be user-specified
  +
 
rcoulomb = 1.0 #distance for the Coulomb cut-off
 
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)
 
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.
 
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.
 
pbc = no #Use no periodic boundary conditions, ignore the box.

Latest revision as of 21:59, 25 June 2012

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.