nitial MD of cys
 &cntrl
  iwrap = 1,
  imin = 0,
  irest = 0,
  ntx = 1,
  nstlim = 5000000,
  dt = 0.002,
  ntwx = 1000,
  ntpr = 1000,
  ntb =2,
  ntc=2,
  ntf=2,
  cut = 8,
  ntt = 3,
  ntp=1,
  pres0=1,
  taup=3,
  gamma_ln = 2.0,
  temp0 = 298.15,
  &end