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:
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb=1,
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,
nscm=1,
&end
Any response will be high appreciated. Thank you.
Best,
Xiaowei Li
University of Virginia
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Received on Wed Nov 22 2006 - 06:07:24 PST
