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. Author manuscript; available in PMC: 2016 Jan 1.
Published in final edited form as: Methods Mol Biol. 2015;1215:253–287. doi: 10.1007/978-1-4939-1465-4_12
aMD production run
  &cntrl
   imin=0, irest=1, ntx=7,
   ntb = 2, pres0 = 1.0, ntp = 2, taup = 2.0,
   cut = 12.0,
   ntr = 0,
   ntc = 2, ntf = 2,
   tempi = 310.0, temp0 = 310.0,
   ntt = 3, gamma_ln = 1.0,
   nstlim = 500000, dt = 0.002
   ntpr = 2000, ntwx = 2000, ntwr = 2000
   iamd = 3,
   alphaD = 357.7,
   EthreshD = 12988.9,
   alphaP= 10494.2,
   EthreshP = -94241.8
  /