Sample control file

MD simulation in the NVE ensemble with the CHARMM, AMBER, and coarse-grained (CG) force fields

If you use different force fields, only [INPUT] and [ENERGY] sections are differently specified, and other sections are basically common. In this page, we show sample control files for CHARMM, AMBER, and coarse-grained force fields.

CHARMM force field

In order to use the CHARMM force fields, we need to specify topfile and parfile (and strfile if needed) in the [INPUT] section. Topology and parameter files are available from the MacKerell’s homepage. To prepare input psffile and pdbfile, we usually utilize psfgen, VMD, or CHARMM. In the [ENERGY] section, forcefield = CHARMM is used, and vdw_force_switch = YES is recommended for the CHARMM C36 force field.

[INPUT]
topfile  = top_all36_prot.rtf, top_all36_lipid.rtf  # topology file
parfile  = par_all36_prot.prm, par_all36_lipid.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          # GENESIS 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      # Leapfrog Verlet integrator
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         = NVE       # NVE ensemble
tpcontrol        = NO        # No thermostat and barostat
temperature      = 300.0     # initial temperature (K)

[BOUNDARY]
type             = PBC       # periodic boundary condition


AMBER force field

In order to use the AMBER force fields, we need to specify prmtopfile and coordinates file (ambcrdfile or/and pdbfile; if both of them specified, coordinates in ambcrdfile will be ignored). The input files can be created with LEaP module of AmberTools.

  • Velocities and periodic box size in ambcrdfile are always ignored in GENESIS.
    • The initial box size of the simulation is given by box_size_x, y, and z in the [BOUNDARY] section, or loaded from rstfile in the [INPUT] section.
  • In the [ENERGY] section, forcefield = AMBER must be specified
    • switchdist and cutoffdist must be the same value.
  • Pay special attention on water_model in [CONSTRAINTS] section, where water_model = WAT should be specified if your system has water molecules named “WAT”.
[INPUT]
prmtopfile  = input.prmtop         # input prmtop file
ambcrdfile  = input.inpcrd         # amber crd file
pdbfile     = input.pdb            # pdb file
rstfile     = minimized.rst        # GENESIS restart

[OUTPUT]
dcdfile     = md.dcd
rstfile     = md.rst

[ENERGY]
forcefield       = AMBER     # AMBER force field
electrostatic    = PME       # Particle Mesh Ewald method
switchdist       = 8.0       # switch distance
cutoffdist       = 8.0       # cutoff distance
pairlistdist     = 10.0      # pair-list distance
pme_nspline      = 4         # order of B-spline in [PME]
pme_max_spacing  = 1.0       # max grid spacing 

[DYNAMICS]
integrator       = LEAP      # Leapfrog Verlet integrator
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
water_model      = WAT       # water molecule name

[ENSEMBLE]
ensemble         = NVE       # NVE ensemble
tpcontrol        = NO        # No thermostat and barostat
temperature      = 300.0     # initial temperature (K)

[BOUNDARY]
type             = PBC       # periodic boundary condition


Coarse-grained force fields (MARTINI, Cα Go, all-atom Go)

(coming soon!)