Second Equilibration Stage in Explicit Solvent &cntrl ntt=3, ! Temperature scaling (=3, Langevin dynamics) gamma_ln=2.0, ! Collision frequency of the Langevin dynamics in ps-1 ntc=2, ! SHAKE constraints (=2, hydrogen bond lengths constrained) ntf=2, ! Force evaluation (=2, hydrogen bond interactions omitted) ntb=1, ! Boundaries (=1, constant volume) cut=8.0, ! Cutoff dt=0.002, ! The time step in picoseconds nstlim=10000000, ! Number of MD steps to be performed ig=-1, ! Random seed (=-1, get a number from current date and time) ntwr=10000, ! Restart file written every ntwr steps ntwx=10000, ! Trajectory file written every ntwx steps ntpr=10000, ! The mdout and mdinfo files written every ntpr steps ioutfm=1, ! Trajectory file format (=1, Binary NetCDF) iwrap=1, ! Translate water molecules into the original simulation box igb=0, ! GB model (=0, explicit solvent) saltcon=0.1, ! Salt concentration irest=1, ! Flag to restart the simulation ntx=5, ! Initial condition (=5, coord. and veloc. read from the inpcrd file) ntr=1, ! Turn on positional restraints restraintmask='@CA,C,O,N|(:HEH,PRN)@FE,NA,NB,NC,ND,C3D,C2A,C3B,C2C,CA,CB', restraint_wt=0.1, ! 0.1 kcal/mol.A**2 restraint force constant /