[gmx-developers] question about energy fluctuation

Qiao Baofu qiaobf at gmail.com
Wed Nov 8 17:33:44 CET 2006

Hi all,

After running a MD of a system with about 17000 atoms, I calculated the
potential and the total-energy:

Last frame read 1557952 time 1557.952

Statistics over 1557953 steps [ 0.0000 thru 1557.9520 ps ], 2 data sets

Energy                      Average       RMSD     Fluct.      Drift

Potential                   -273047    626.559    611.258  -0.305998   -
Total-Energy                -184656    839.662    828.307  -0.305999   -

I found that the Fluct./Average is 0.45% (Total-Energy), 0.22%(Potential).
In the simulation, the time step is 0.001ps, and I saved the energy every

On the other hand, on page 98 of the book "Computer Simulation of Liquids"
(M. P. Allen & D. J. Tildesley), it is said "For a simple Lennard-Jones
system, fluctuation of order 1 part in 10^4 are generally considered to be

The ratio obtained from Gromacs are quite bigger.  Therefore, I want to know
if there are any standard for different system to check whether the system
are accetable or not.

PS: Another question: I found only when the energy data are divided by the
number of the molecules, the obtained result are consistent with the date in
some related papers. In Gromacs, the unit of energy is KJ/mol. If divided by
the number of molecules, how to consider the unit?

Thanks for any suggestions!

Sincerely yours,
Baofu Qiao, PhD
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