Sample control file
REUS (or Hamiltonian REMD) simulation using a distance restraint
REUS simulation can be done by just adding the [REMD] section in the control file of the conventional MD simulation with restraints and modifying the [INPUT]/[OUTPUT] sections. The following sample is a REUS simulation using distance restraints with 6 replicas. During the simulation, force constants and target distance values are exchanged between replicas. Note that the parameter rest_function in the [REMD] section points out the index of restraint function defined in the [RESTRAINTS] section.
[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 = 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 = 2500 # attempt exchange every 5 ps
type1 = RESTRAINT # restraint function is exchanged
nreplica1 = 6 # number of replicas
rest_function1 = 1 # target restraint function index
[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 = 50000 # number of MD steps
timestep = 0.002 # timestep (ps)
eneout_period = 100 # energy output period
crdout_period = 100 # coordinates output period
rstout_period = 50000 # 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 = 300.0 # target temperature (K)
gamma_t = 1.0 # thermostat friction coefficient (ps-1)
[BOUNDARY]
type = PBC # periodic boundary condition
[SELECTION]
group1 = an:N and resno: 1 # select atom i
group2 = an:O and resno: 10 # select atom j
[RESTRAINTS]
nfunctions = 1
function1 = DIST # use distance restraint
select_index1 = 1 2 # restrained atom index i and j
constant1 = 10 10 10 10 10 10 # force constant of each replica
reference1 = 4.0 4.3 4.5 4.7 4.9 5.1 # target distance of each replica
In this case, we define parameter1 = (10, 4.0), parameter2 = (10, 4.3), …, and parameter6 = (10, 5.1), and each replica has one of these parameters.