Heating Stage in Implicit Solvent &cntrl ntt=3, ! Temperature scaling (=3, Langevin dynamics) gamma_ln=5.0, ! 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=0, ! Boundaries (=0, non-periodic) cut=1000.0, ! Cutoff dt=0.002, ! The time step in picoseconds nstlim=1500000, ! 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) igb=2, ! GB model saltcon=0.1, ! Salt concentration 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=1.0, ! 1 kcal/mol.A**2 restraint force constant nmropt=1, ! To vary target temperature below / &wt TYPE='TEMP0', ISTEP1=0, ISTEP2=300000 VALUE1=10.00, VALUE2=300.0, / &wt TYPE='END' /