[gmx-users] md.log question
David van der Spoel
spoel at xray.bmc.uu.se
Sun Feb 10 23:04:41 CET 2002
On Sun, 10 Feb 2002, Rui Qiao wrote:
> I am doing some simulation using Gromacs, when I look at the
>md.log file today, I find that the energy has a NaN there, i.e.
> Energies (kJ/mol)
> LJ (SR) Coulomb (SR) Coulomb (LR) Potential Kinetic
> nan nan -3.76832e+04 nan
> Total Energy Temperature Pressure (bar)
> nan 2.99925e+02 6.97891e+02
> Step Time Lambda Annealing
> 5000 7.50000 0.00000 1.00000
> What a nan means? Also, why the pressure is so high? My simulation
>is some water molecular in a channel (water density 1g/cm^3).
NaN means "Not a Number"
You probably have some problem with very large forces. Depends on your
system of course.
The pressure is not very high, it usually fluctuates quite a bit.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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