Sample control file
MD simulation of a biological membrane in the NPT, NPAT, and NPγT ensembles
In order to use NPT, NPAT, or NPγT, [ENSEMBLE]
section is modified. Note that isotropy = ISO
, ANISO
, and SEMI-ISO
are available for the NPT and NPγT ensembles, and XY-FIXED
is for the NPAT ensemble. In the simulations of biological membranes and membrane proteins, semi-isotopic pressure coupling in the NPT ensemble is usually used. In the samples below, we use the Langevin thermostat and barostat. Other algorithms such as Berendsen and Bussi thermostat/barostat are also available with these ensembles.
NPT ensemble
[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 # 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 = NPT # NPT ensemble tpcontrol = LANGEVIN # thermostat and barostat temperature = 323.15 # initial and target temperature (K) pressure = 1.0 # initial and target pressure (atm) 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
NPAT ensemble
[ENSEMBLE]
ensemble = NPAT # NPAT ensemble
tpcontrol = LANGEVIN # thermostat and barostat
temperature = 323.15 # temperature (K)
pressure = 1.0 # normal pressure (atm)
isotropy = XY-FIXED # XY dimensions are fixed
gamma_t = 1.0 # thermostat friction coefficient (ps-1)
gamma_p = 0.1 # barostat friction coefficient (ps-1)
NPγT ensemble
[ENSEMBLE]
ensemble = NPgT # NPgammaT ensemble
tpcontrol = LANGEVIN # thermostat and barostat
temperature = 323.15 # temperature (K)
pressure = 1.0 # normal pressure (atm)
gamma = 20.0 # surface tension (dyn/cm)
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)