Popov Konstantin wrote:
Hello,
I run simulations with polyethylene molecules with harmonic potential for C-H
bonds and Morse potential for C-C bonds. The system consists of 1000 carbon
atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density
(~0.8 g cm-3) and no pressure coupling. At the temperature 2900 K about 25% of
simulations end up with NAN (not a number) records in their .log and .gro
files. Simulations for the same system at the same temperature in vacuum don't
have this problem. Simulations run with the same density but lower temperature
(2500 K) don't have this problem either.
Below is a fragment of a .log file when reasonable numbers turn to NANs:
Step Time Lambda
14780 14.78000 0.00000
Energies (kJ/mol)
Bond Morse Angle Ryckaert-Bell. LJ (SR)
2.62634e+04 1.84883e+04 5.57324e+04 6.74611e+03 5.36911e+03
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
6.11740e+02 1.13211e+05 1.12145e+05 2.25356e+05 2.99729e+03
Pressure (bar)
1.49525e+04
Step Time Lambda
14790 14.79000 0.00000
Group rest with mass 1.40287e+04, Ekrot 8.82852e+00 Det(I) = 1.54313e+12
COM: 1.56520 1.58669 1.58357
P: -0.00208 0.00121 0.00119
V: -0.00000 0.00000 0.00000
J: 560.09625 -303.20575 13.91409
w: 0.02418 -0.01353 0.00097
Inertia tensor (3x3):
Inertia tensor[ 0]={ 1.13658e+04, -2.64121e+02, 1.90793e+02}
Inertia tensor[ 1]={-2.64121e+02, 1.17820e+04, -2.87465e+02}
Inertia tensor[ 2]={ 1.90793e+02, -2.87465e+02, 1.15395e+04}
Energies (kJ/mol)
Bond Morse Angle Ryckaert-Bell. LJ (SR)
2.48452e+04 1.71570e+04 5.62121e+04 6.85057e+03 5.75860e+03
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
6.03772e+02 1.11427e+05 1.13892e+05 2.25319e+05 3.04398e+03
Pressure (bar)
2.24204e+04
Step Time Lambda
14800 14.80000 0.00000
Energies (kJ/mol)
Bond Morse Angle Ryckaert-Bell. LJ (SR)
nan nan nan nan 0.00000e+00
Coulomb (SR) Potential Kinetic En. Total Energy Temperature
0.00000e+00 nan nan nan nan
Pressure (bar)
nan
Does anybody have any idea what might cause this?
Looks like the simulation is probably exploding. Have a look at the trajectory
to see. NaN is probably an indication of infinite quantities, i.e. some
component of your system has gone shooting off across space. Most likely this
is a consequence of the extreme high temperature; you're probably getting some
fast conformational changes and increasing the likelihood of inter- and
intramolecular clashes.
-Justin
Thanks
K. Popov
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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