[gmx-users] NAN at high temperatures and high pressures

[Justin A. Lemkul]

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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-- 
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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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