【Amber】QM/MM-D-ABMD

在自适应有偏分子动力学过程中加入ORCA处理QM部分计算反应自由能的输入文件

输入文件

预模拟

Input file for pre-MD
&cntrl
  imin = 0, irest = 0, igb = 0, dielc = 1.0,
  ntx  = 1, ntb   = 2, ntt = 3, ntp = 1
  temp0 = 300.0, tautp = 2.0,
  tol = 0.00001, ntc = 2, ntf = 2, iwrap = 1
  cut = 9.0, ibelly = 0, dt = 0.002, gamma_ln=1.0
  ntpr = 5000,
  ntwr = 5000,
  ntwx = 5000,
  nstlim = 250000,
  nscm = 100, infe = 0,
  ntr = 0, ipol = 0
&end

正式模拟

QM/MM-DABMD
 &cntrl
  imin = 0, irest = 0, igb = 0, dielc = 1.0,
  ntx  = 1, ntb   = 1, ntt = 3, ntp = 0
  temp0 = 300.0, tautp = 2.0,
  tol = 0.00001, ntc = 2, ntf = 2, iwrap = 1
  cut = 9.0, ibelly = 0, dt = 0.0001, gamma_ln=1.0
  ntpr = 1,
  ntwr = 1,
  n