Hemochromatosis gromacs mdp

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-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.


GBSA

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

energygrps:

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.