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)