Hemochromatosis gromacs mdp
Revision as of 12:18, 24 June 2012 by Joerdensv (Created page with "-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 incl…")
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].
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
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.
Twin range cut-off’s with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb�>rlist.
Twin range cut-off’s with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw >= rlist.
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.
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.