AMBER Archive (2003)

Subject: AMBER: large changes in xyz coordinates

From: Sivakolundu, Sivashankar (Sivashankar.Sivakolundu_at_stjude.org)
Date: Sat Aug 16 2003 - 20:06:14 CDT

Hi amber users,
I'm trying to do an constant pressure md simulation of a protein solvated in a water box using Amber 7 for several nanoseconds. The simulation went fine until it was around 8 ns and then it crashed without any error message. I couldn't restart the simulation since the restart file didnt seem to have any coordinates (see below), though the values for velocities looked fine.

When I examined the coordinate trajectory file, I noticed that the value of x, y, and, z coordinates were in the order of 1000-9000 few steps before the crash. The value of starting coordinates for this simulation was in the order of 10-20. As the simulation proceeded, the value seem to slowly increase. Is it the translational/rotational motion of the molecule? I was wondering whether the simulation crashed when it ran out of formatted space allocated for the coordinates in the file.

Could anyone provide some insights into what was wrong with my simulation? Please let me know if you need more info.

My instruction file for the simulation looked as follows:
 # MD with constant pressure and temperature
 &cntrl

  ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 1000, ntwe = 100,

  ntf = 2, ntb = 2,
  cut = 9.0, nsnb = 10,

  imin = 0,
  nstlim = 5000000,
  nscm = 0,
  t = 0.0, dt = 0.002,

  tempi=300., temp0 = 300.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 3,
  vlimit = 20.0,
  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 1.0, npscal = 1,

  ntc = 2, tol = 0.000001,
 &end

The first few lines of restart file looked as follows:

10779 0.8238000E+04
************************4533.5703286************************4533.6510501
************************4532.8629810************************4533.1942804
************************4534.8782461************************4535.2767871
************************4534.5460759************************4533.7682646
************************4534.1354013************************4535.6734788
************************4536.6514430************************4535.7368984
************************4535.4929706************************4535.6541993
************************4536.2869418************************4534.1083471
************************4534.1167581************************4533.3567749
************************4533.8220697************************4534.1218930
************************4534.2912817************************4532.8311031
************************4535.9055763************************4535.7103922
************************4537.0996446************************4538.3389121
************************4538.4410702************************4538.3509233
************************4539.5048365************************4540.4037295

The info output file just stopped at the last step without any error message.

Any suggestions will be appreciated.

Thank you very much

Siva Sivakolundu
Postdoc, SJCRH,
Memphis, TN 38103

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