Recommended control parameters in ver. 1.4
Contents
The followings are recommended control parameters in GENESIS ver. 1.4 to carry out normal all-atom MD simulations in explicit solvent with the CHARMM and AMBER force fields. In this version, we recommend the users to employ VRES integrator with 2.5 fs for production runs, since it is more efficient than the traditional protocol (LEAP or VVER with 2.0 fs). In addition, BUSSI thermostat and barostat are recommended, since the method can reproduce transport properties and kinetics in the MD simulations more accurately than the others (see J. E. Basconi and M. R. Shirts, J. Chem. Theory Comput., 2013)
MD simulation in explicit solvent with CHARMM FF (NVT)
[ENERGY] forcefield = CHARMM # CHARMM force field electrostatic = PME # use Particle mesh Ewald method switchdist = 10.0 # switch distance cutoffdist = 12.0 # cutoff distance pairlistdist = 13.5 # pair-list distance pme_nspline = 4 # order of the spline interpolation vdw_force_switch = YES # turn on vdw force switch pme_max_spacing = 1.2 # Max grid spacing allowed [DYNAMICS] integrator = VRES # [LEAP,VVER,VRES] timestep = 0.0025 # timestep (ps) nbupdate_period = 10 # pairlist update period elec_long_period = 2 # period of reciprocal space calculation thermostat_period = 10 # period of thermostat update barostat_period = 10 # period of barostat update [CONSTRAINTS] rigid_bond = YES # use SHAKE/RATTLE fast_water = YES # use SETTLE [ENSEMBLE] ensemble = NVT # [NVE,NVT,NPT] tpcontrol = BUSSI # thermostat and barostat temperature = 300 # K
MD simulation in explicit solvent with CHARMM FF (NPT)
[ENERGY]
forcefield = CHARMM # CHARMM force field
electrostatic = PME # use Particle mesh Ewald method
switchdist = 10.0 # switch distance
cutoffdist = 12.0 # cutoff distance
pairlistdist = 13.5 # pair-list distance
pme_nspline = 4 # order of the spline interpolation
vdw_force_switch = YES # turn on vdw force switch
pme_max_spacing = 1.2 # Max grid spacing allowed
[DYNAMICS]
integrator = VRES # [LEAP,VVER,VRES]
timestep = 0.0025 # timestep (ps)
nbupdate_period = 10 # pairlist update period
elec_long_period = 2 # period of reciprocal space calculation
thermostat_period = 10 # period of thermostat update
barostat_period = 10 # period of barostat update
[CONSTRAINTS]
rigid_bond = YES # use SHAKE/RATTLE
fast_water = YES # use SETTLE
[ENSEMBLE]
ensemble = NPT # [NVE,NVT,NPT]
tpcontrol = BUSSI # thermostat and barostat
pressure = 1 # atm
temperature = 300 # K
MD simulation in explicit solvent with AMBER FF (NVT)
[ENERGY] forcefield = AMBER # AMBER force field electrostatic = PME # use Particle mesh Ewald method switchdist = 8.0 # switch distance cutoffdist = 8.0 # cutoff distance pairlistdist = 9.5 # pair-list distance pme_nspline = 4 # order of the spline interpolation pme_max_spacing = 1.2 # Max grid spacing allowed [DYNAMICS] integrator = VRES # [LEAP,VVER,VRES] timestep = 0.0025 # timestep (ps) nbupdate_period = 10 # pairlist update period elec_long_period = 2 # period of reciprocal space calculation thermostat_period = 10 # period of thermostat update barostat_period = 10 # period of barostat update [CONSTRAINTS] rigid_bond = YES # use SHAKE/RATTLE fast_water = YES # use SETTLE water_model = WAT # define TIP3P residue name [ENSEMBLE] ensemble = NVT # [NVE,NVT,NPT] tpcontrol = BUSSI # thermostat and barostat temperature = 300 # K
MD simulation in explicit solvent with AMBER FF (NPT)
[ENERGY] forcefield = AMBER # AMBER force field electrostatic = PME # use Particle mesh Ewald method switchdist = 8.0 # switch distance cutoffdist = 8.0 # cutoff distance pairlistdist = 9.5 # pair-list distance pme_nspline = 4 # order of the spline interpolation pme_max_spacing = 1.2 # Max grid spacing allowed [DYNAMICS] integrator = VRES # [LEAP,VVER,VRES] timestep = 0.0025 # timestep (ps) nbupdate_period = 10 # pairlist update period elec_long_period = 2 # period of reciprocal space calculation thermostat_period = 10 # period of thermostat update barostat_period = 10 # period of barostat update [CONSTRAINTS] rigid_bond = YES # use SHAKE/RATTLE fast_water = YES # use SETTLE water_model = WAT # define TIP3P residue name [ENSEMBLE] ensemble = NPT # [NVE,NVT,NPT] tpcontrol = BUSSI # thermostat and barostat pressure = 1 # atm temperature = 300 # K