MD simulation

&cntrl

imin=0, ! Perform MD

nstlim=50000 ! Number of MD steps

!nstlim=500 ! Number of MD steps

ntx=5, ! Positions and velocities read formatted

irest=1, ! Restart calculation

ntc=1, ! No SHAKE on for bonds with hydrogen

dt=0.001, ! Timestep (ps)

ntb=2, ! Constant Pressure

ntp=1, ! Isotropic pressure scaling

barostat=1 ! Berendsen

taup=0.5 ! Pressure relaxtion time (ps)

ntf=1, ! Complete force evaluation

ntt=3, ! Langevin thermostat

gamma_ln=2.0 ! Collision Frequency for thermostat

ig=-1, ! Random seed for thermostat

temp0=310 ! Simulation temperature (K)

ntwx= 1000, ! Write to trajectory file every ntwx steps

ntpr= 1000, ! Print to mdout every ntpr steps

ntwr= 1000, ! Write a restart file every ntwr steps

cut= 8.0, ! Nonbonded cutoff in Angstroms

ntr=1, ! Turn on restraints

restraintmask=":1-1000@CA,C,N", ! atoms to be restrained

restraint_wt=0.1, ! force constant for restraint

ntxo=1, ! Write coordinate file in ASCII format

ioutfm=0, ! Write trajectory file in ASCII format

iwrap=1, ! iwrap is turned on

&end