AMBER Archive (2003)

Subject: AMBER: DNA helix is not in z-direction

From: A. Hungie (hungie01_at_hotmail.com)
Date: Fri Sep 05 2003 - 04:35:50 CDT

Dear All,

I am using AMber 6 with parm94.dat force field. I have done simulation of
DNA in water box (and also Na+ ions). The starting configuration was that
the DNA was in the middle of the box and its axis was in z-derection. After
production run, I found that the rectangular box was still in z-direction
and center of mass of DNA also still in the middle of the box, but the DNA
axis leaned about 30-40 degree with respect to z-axis. Could any one suggest
  me how to run simulation that the main axis of DNA still is in z-directin?
The input file as below. Thank you very much in advance.

Sincerely Yours,
Hungie

-----------------
&cntrl

  ntx = 7, irest = 1, nmropt = 0,
  imin = 0,
  ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
  nstlim = 800000,
  dt = 0.001, ndfmin = 0, t = 0.0,
  timlim = 999999., ntcm = 1, nscm = 2500,
  ntpr = 1000, ntwr = 1000,
  ntwx = 1000, ntwv = 0, ntwe = 0,
  ntwprt = 0, ioutfm = 0, ntrx = 1, ntxo = 1,
  cut = 8.0, dielc = 1.0, nsnb = 10,
  scnb = 2.0, scee = 1.2, iwrap = 0,
  ntb = 1, ntp = 0, npscal = 1,
  pres0 = 1.0, comp = 44.6, taup = 2.0,
  ntc = 2, tol = 0.000001,
  ntf = 2,
  ibelly = 0, ntr = 0,
  temp0 = 300.0, tempi = 300.0,
  ig = 71277, heat = 0.0, tautp = 4.0,
  ntt = 0, vlimit = 20.0, dtemp = 0.0,
&end

&ewald
  a = 42.1307275, b = 43.1931490, c = 69.7138947,
  alpha = 90.000, beta = 90.000, gamma = 90.000,
  nfft1 = 45, nfft2 = 45, nfft3 = 72,
  order = 4, dsum_tol = 0.000001, eedmeth = 1,
  opt_infl = 1, vdwmeth = 1, use_pme = 1,
  frc_int = 0, nbflag = 1, skinnb = 1.0
&end

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