min_relax.inp

mini_nstep  = 5000                              # Number of steps for minimization
mini_Tol    = 100.0                             # Minimization energy tolerance
                                         
gen_vel     = yes                               # Generate initial velocities
gen_temp    = 310                            # Temperature for generating initial velocities (K)
                                         
nstep       = 1000000                            # Number of steps to run
dt          = 0.002                             # Time-step (ps)
                                         
nstout      = 5000                              # Writing output frequency (steps)
nstdcd      = 5000                              # Writing coordinates trajectory frequency (steps)
                                         
coulomb     = PME                               # Electrostatic cut-off method
ewald_Tol   = 0.0005                            # Ewald error tolerance
vdw         = CutoffPeriodic                    # vdW cut-off method
lj_lrc      = yes
r_off       = 0.9                               # Switch-off distance (nm)
                                         
temp        = 310                            # Temperature (K)
fric_coeff  = 1                                 # Friction coefficient for Langevin dynamics
                                         
pcouple     = no                                # Turn on/off pressure coupling
                                         
cons        = HBonds                            # Constraints method
                                         
rest        = yes                               # Turn on/off restraints
fc_bb       = 400.0                             # Positional restraint force constant for protein backbone (kJ/mol/nm^2)
fc_sc       = 40.0                              # Positional restraint force constant for protein side-chain (kJ/mol/nm^2)