Sample control file
MD simulation of a small peptide in vacuum in the canonical ensemble (atdyn only)
Because spdyn is only applicable to periodic boundary condition (PBC), atdyn is used for a non-periodic boundary condition (NOBC). In the NOBC simulation, isobaric-isothermal ensemble (NPT) is not available. In addition, the volume (V) is not considered even if NVE or NVT is specified in the keyword “ensemble”.
[INPUT] topfile = top_all36_prot.rtf # topology file parfile = par_all36_prot.prm # parameter file psffile = peptide.psf # protein structure file pdbfile = peptide.pdb # input PDB file [OUTPUT] dcdfile = md.dcd # DCD trajectory file rstfile = md.rst # restart file [ENERGY] forcefield = CHARMM # CHARMM force field electrostatic = CUTOFF # Particle Mesh Ewald method switchdist = 28.0 # switch distance cutoffdist = 30.0 # cutoff distance pairlistdist = 32.0 # pair-list distance vdw_force_switch = YES # force switch option for van der Waals [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 stoptr_period = 1000 # remove translation and rotation of COM rstout_period = 10000 # restart output period nbupdate_period = 10 # nonbond update period [CONSTRAINTS] rigid_bond = YES # constraints all bonds involving hydrogen [ENSEMBLE] ensemble = NVT # NVT ensemble tpcontrol = LANGEVIN # thermostat temperature = 298.15 # initial and target temperature (K) gamma_t = 1.0 # thermostat friction coefficient (ps-1) [BOUNDARY] type = NOBC # No boundary condition