MD 1ns
 &cntrl
   ntc=2,			!Shake Alg.
   ntf=2,			!Force evaluation, bond H omitted
   cut=300,			!Non bonded cutoff		
   igb=1,			! GB		
   gbsa=1,			!GBSA with hydrophobic effects
   ntpr=5000,			!print intermediate results every
   ntwx=5000,			!write every
   ntwr=5000,			!write restart every
   nstlim = 500000,		!step (1ns)
   dt=0.002,			!timestep
   ntt=1,			!Constant T using the weak coupling
   temp0=300.0,			!T
   tautp=2.0,			!time costant(ps) for bath coupling
   ntx=5,			!read initial coordinate and velocities
   irest=1,			!Read the vlocities to resume the simulation
   ntb=0,			! NO PBC
   nscm = 5000,			!remove Tr/rot dt
 /