Sample control file
Surface-tension REMD simulation for a membrane system
Note that the NPγT ensemble is used in surface-tension REMD, where the temperature and normal pressure in each replica is specified in the [ENSEMBLE] section.
[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 = eq_rep{}.rst # restart file
[OUTPUT]
logfile = run_rep{}.log # log file
dcdfile = run_rep{}.dcd # coordinates trajectory file
rstfile = run_rep{}.rst # restart file
remfile = run_rep{}.rem # parameter index file
[REMD]
dimension = 1 # Number of dimension of REMD simulation
exchange_period = 5000 # attempt exchange every 10 ps
type1 = GAMMA # Surface tension exchange
nreplica1 = 5 # Number of replicas
parameters1 = -10.0 -5.0 0.0 5.0 10.0 # target surface tension (dyn/cm)
[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 = 500000 # number of MD steps
timestep = 0.002 # timestep (ps)
eneout_period = 100 # energy output period
crdout_period = 100 # coordinates output period
rstout_period = 500000 # restart output period
nbupdate_period = 10 # nonbond update period
[CONSTRAINTS]
rigid_bond = YES # constraints all bonds involving hydrogen
[ENSEMBLE]
ensemble = NPgT # NPgammaT ensemble
tpcontrol = LANGEVIN # thermostat
temperature = 323.15 # target temperature
pressure = 1.0 # target normal pressure
isotropy = SEMI-ISO # semi-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