AMBER Archive (2003)

Subject: Etot is not constant in NVE ensemble

From: A. Hungie (hungie01_at_hotmail.com)
Date: Fri May 09 2003 - 08:46:43 CDT

Dear All,

I have run MD simulation of 14 basepairs DNA (in water and nuetralized by
Na+ ions) using protocol as in Amber tutorial. After doing 6 rounds of
minimizations (reducing restrain energy from 25 to 0 kcal/mol.A^2), I ran MD
in NPT ensemble for 100 ps which I obtained canstant box size. Then I
switched to NVE ensemble for 5.6 ns (800 ps for each run). I found that
total energy is not constant, i.e. it increases about 6 kcal/mol (from
-37828 kacl/mol to -37822 kcal/mol) within 5.6 ns. I used Amber 6 on Linux
cluster and input file as below.

Is the obtained total energy normal and acceptable? Is it equilibrium?

#my input file.
------------------------------------------
&cntrl
  ntx = 7, irest = 1, nmropt = 0,
  imin = 0,
  maxcyc = 1000, ncyc = 5000,
  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 = 1.0,
&end

&ewald
  a = 42.0151161, b = 43.0746222, c = 69.8275997,
  alpha = 90.000, beta = 90.000, gamma = 90.000,
  nfft1 = 45, nfft2 = 45, nfft3 = 72,
  order = 4, dsum_tol = 0.00001, eedmeth = 1,
  opt_infl = 1, vdwmeth = 1, use_pme = 1,
  frc_int = 0, nbflag = 1, skinnb = 1.0
&end
-----------------------------------

Thank you very much in advance.

Hungie

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