Sample control file
MD simulation in the NPT ensemble with Langevin, Berendsen, and Bussi thermostat and barostat
In GENESIS, three types of thermostat and barostat are available: Langevin, Berendsen, and Bussi (Stochastic velocity rescaling) methods. Available combinations between thermostats/barostats and integrators are as follows:
Thermostat/barostat | Integrator |
LANGEVIN | LEAP, VVER |
BERENDSEN | LEAP |
BUSSI | VVER |
Thermostat/barostat is specified by tpcontrol
in the [ENSEMBLE]
section, and integrator is specified by integrator
in the [DYNAMICS]
section. To control the temperature and pressure, gamma_t
and gamma_p
are used in LANGEVIN
, and tau_t
and tau_p
are used in BERENDSEN
and BUSSI
.
In GENESIS, different types of thermostat and barostat cannot be combined. For example, Langevin thermostat with Berendsen barostat is not available.
Langevin thermostat and barostat
[INPUT]
topfile = top_all36_prot.rtf # topology file
parfile = par_all36_prot.prm # parameter file
strfile = toppar_water_ions.str # stream file
psffile = ionized.psf # protein structure file
pdbfile = ionized.pdb # input PDB file
rstfile = minimized.rst # restart file
[OUTPUT]
dcdfile = md.dcd # DCD trajectory file
rstfile = md.rst # restart file
[ENERGY]
forcefield = CHARMM # CHARMM force field
electrostatic = PME # Particle Mesh Ewald method
switchdist = 10.0 # switch distance
cutoffdist = 12.0 # cutoff distance
pairlistdist = 13.5 # pair-list distance
vdw_force_switch = YES # force switch option for van der Waals
pme_nspline = 4 # order of B-spline in [PME]
pme_max_spacing = 1.0 # max grid spacing
[DYNAMICS]
integrator = LEAP # [LEAP,VVER]
nsteps = 10000 # number of MD steps
timestep = 0.002 # timestep (ps)
eneout_period = 100 # energy output period
crdout_period = 100 # coordinates output period
rstout_period = 10000 # restart output period
nbupdate_period = 10 # nonbond update period
[CONSTRAINTS]
rigid_bond = YES # constraints all bonds involving hydrogen
[ENSEMBLE]
ensemble = NPT # NPT ensemble
tpcontrol = LANGEVIN # thermostat/barostat
temperature = 300.0 # target temperature (K)
pressure = 1.0 # target pressure (atm)
isotropy = ISO # isotropic pressure coupling
gamma_t = 1.0 # thermostat friction coefficient (ps-1)
gamma_p = 0.1 # barostat friction coefficient (ps-1)
[BOUNDARY]
type = PBC # periodic boundary condition
Berendsen thermostat and barostat
[DYNAMICS] integrator = LEAP # [LEAP] nsteps = 10000 # number of MD steps timestep = 0.002 # timestep (ps) eneout_period = 100 # energy output period crdout_period = 100 # coordinates output period rstout_period = 10000 # restart output period nbupdate_period = 10 # nonbond update period [ENSEMBLE] ensemble = NPT # NPT ensemble tpcontrol = BERENDSEN # thermostat/barostat temperature = 300.0 # target temperature (K) pressure = 1.0 # target pressure (atm) isotropy = ISO # isotropic pressure coupling tau_t = 5.0 # temperature coupling time (ps) tau_p = 5.0 # pressure coupling time (ps) compressibility = 0.0000463 # compressibility (atm-1)
Bussi thermostat and barostat (Stochastic velocity rescaling method)
[DYNAMICS] integrator = VVER # [VVER] nsteps = 10000 # number of MD steps timestep = 0.002 # timestep (ps) eneout_period = 100 # energy output period crdout_period = 100 # coordinates output period rstout_period = 10000 # restart output period nbupdate_period = 10 # nonbond update period [ENSEMBLE] ensemble = NPT # NPT ensemble tpcontrol = BUSSI # thermostat/barostat temperature = 300.0 # target temperature (K) pressure = 1.0 # target pressure (atm) isotropy = ISO # isotropic pressure coupling tau_t = 5.0 # temperature coupling time (ps) tau_p = 5.0 # pressure coupling time (ps)