AMBER Archive (2003)

Subject: AMBER: vlimit?

From: Ran Ye (ryejob_at_yahoo.com)
Date: Sun Dec 21 2003 - 16:15:57 CST

Hi, Amber users-

I'm basically following the steps on the "DNA"
tutorial
to do some MD on proteins. I couldn't get my dynamics
going because "vlimit exceeded" and "Coordinate
resetting (SHAKE) cannot be accomplished". Does anyone
know how to fix it?

Appreciate!

Here's my "md_ntr.in" file:

-------------------
 &cntrl

  nmropt = 0,
  ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0,
ntwe = 0,

  ntf = 2, ntb = 2,
  cut = 8.0, nsnb = 10,

  ibelly = 0, ntr = 1,

  imin = 0,
  nstlim = 250,
  nscm = 0,
  t = 0.0, dt = 0.002,

  temp0 = 263.15, tempi = 263.15,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,

  ntc = 2, tol = 0.00001

 &end
Hold the protein fixed
500.0
RES 1 88
END
END

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