[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:

>Dear All:
>       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.

Groeten, David.
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

More information about the gromacs.org_gmx-users mailing list