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陈闹钟

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虫号: 2325240
注册: 2013-03-07
性别: MM
专业: 理论和计算化学

[求助] vlimit exceeded for step 8367; vmax = 22.4965（amber,MD过程中出现错误）

在跑蛋白质的AMBER的平衡过程中出现以下的错误：
vlimit exceeded for step 8367; vmax = 22.4965

   Coordinate resetting (SHAKE) cannot be accomplished,
   deviation is too large
   NITER, NIT, LL, I and J are : 0 2  441  913  914

   Note: This is usually a symptom of some deeper
   problem with the energetics of the system.
输入文件equi.in，如下：

&cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1,
  taup = 2.0,
  cut = 12.0, ntr = 0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  vlimit = 20 ,
  nstlim = 50000, dt = 0.002,
  ntpr = 1, ntwx = 1, ntwr = 1
/

之前heating，cooling,输入文件如下：
heating.in 如下:

  &cntrl
  imin = 0,
  irest  = 0,
  ntx = 1,
  ntb = 1,
  cut = 12.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi  = 0.0,
  temp0  = 450.0,
  ntt = 3,
  vlimit = 20,
  gamma_ln = 1.0,
  nstlim = 60000, dt = 0.0005,
  ntpr = 1000, ntwx = 100, ntwr = 1000,
/
Hold the 2Q6P fixed
0.0
RES 224 340
END
END

cooling.in  如下：

&cntrl
  imin = 0,
  irest  = 0,
  ntx = 1,
  ntb = 1,
  cut = 12.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi  = 450.0,
  temp0  = 300.0,
  ntt = 3,
  vlimit = 20,
  gamma_ln = 1.0,
  nstlim = 60000, dt = 0.0005,
  ntpr = 1000, ntwx = 100, ntwr = 1000,
/
Hold the 2Q6P fixed
0.0
RES 224 340
END
END

同时做minimize的时候，先限制住所有重原子做EM，之后没有任何限制的做EM计算。输入文件如下：
min1_restraint.in  如下：

&cntrl
  imin = 1,
  maxcyc = 500,
  ncyc = 250,
  ntb = 1,
  ntr = 1,
  cut = 12.0,
restraintmask = ':1-223@N,CA,C,N1,C4,C7,C3,C8,N2,C9,C12,N4,C22,C23', restraint_wt = 100.0,
/
Hold the 2Q6P fixed
500.0
RES 224 340
END
END

min2_no_constrain.in 如下：

&cntrl
  imin = 1,
  maxcyc = 50000,
  ncyc = 50000,
  ntb = 1,
  ntr = 0,
  cut = 12.0
/
，请问有人碰过这个问题的吗？知道解决的办法吗？谢谢

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