Hemochromatosis gromacs mdp

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Will tell grompp to include flexible water in stead of rigid water into your topology, this can be useful for normal mode analysis.


Will tell grompp to include posre.itp into your topology, used for position restraints.


Do a simulation with implicit solvent using the Generalized Born formalism. Three
different methods for calculating the Born radii are available, Still, HCT and OBC.
These are specified with the gb_algorithm field. The non-polar solvation is specified
with the sa_algorithm field.

integrator = steep

A steepest descent algorithm for energy minimization. The maximum step size is
emstep [nm], the tolerance is emtol [kJ mol^-1 nm^-1].

nsteps: (0)

maximum number of steps to integrate or minimize, -1 is no maximum

nstenergy: (100) [steps]

frequency to write energies to energy file, the last energies are always written, should be a
multiple of nstcalcenergy. Note that the exact sums and fluctuations over all MD steps
170 Chapter 7. Run parameters and Programs
modulo nstcalcenergy are stored in the energy file, so g_energy can report exact
energy averages and fluctuations also when nstenergy>1


group(s) to write to energy file

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. In large systems grid search is much
faster than simple search.

coulombtype: Cut-off

Twin range cut-off’s with neighborlist cut-off rlist and Coulomb cut-off rcoulomb,
where rcoulomb�>rlist.

vdwtype: Cut-off

Twin range cut-off’s with neighbor list cut-off rlist and VdW cut-off rvdw, where
rvdw >= rlist.

constraints: none

No constraints except for those defined explicitly in the topology, i.e. bonds are represented
by a harmonic (or other) potential or a Morse potential (depending on the
setting of morse) and angles by a harmonic (or other) potential.

pbc: no

Use no periodic boundary conditions, ignore the box. To simulate without cut-offs,
set all cut-offs to 0 and nstlist=0. For best performance without cut-offs, use
nstlist=0, ns_type=simple and particle decomposition instead of domain decomposition.

All these informations were extracted from the Gromacs manual