AMBER Archive (2006)

Subject: AMBER: the energy and temperature both increasing during the simulation with NTT=0

From: Xiaowei (David) Li (
Date: Mon Nov 20 2006 - 12:50:00 CST

Dear Amber Community:

   I have observed that the total system energy and temperature were
increasing in a 10ns production simulation (NVE, NTT=0) of a DNA
decamer. The energy has increased from -63510 to -63410 kcal/mol while
the temperature increased from 300 to 302 K. I thought the temperature
should be stable or drop and the energy should be stable or decrease
because NTT=0 means that there is no energy exchange with external
environment. Correct me if I am wrong, but I am confused by the results.

   Here is my system information and simulation procedure. The system
under simulation is composed of a DNA decamer (and 18 Na+) with a 12
angstrom cubic water box. Before the production simuation, the system
was carefully equilibrated by exactly following the equilibration
procedure described by Beveridge et al. ( D. L. Beveridge, et al. "
Molecular Dynamics Simulations of 136 Unique Tetranucleotide Sequences
of DNA Oligonucleiotides. I. Research Design and Results on d(CpG)
Steps," Biophy. J., vol. 87, pp.3799-3813, Decemeber, 2004).
Specifically, the equilibration procedure includes initial energy
minimization , "heat up" to 300K , and 5 series of 1000 steps energy
minimization and 50 ps NPT equlibration. After the equlibration, the
production simulation starts with following input file:

  imin = 0,
  irest = 1,
  ntx = 5,
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 0,
  nstlim =500000,
  dt = 0.002,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,

Any response will be high appreciated. Thank you.

Xiaowei Li
University of Virginia

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