# [gmx-users] question about energy fluctuation

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 9 02:38:57 CET 2006

```Qiao Baofu wrote:
> 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
> Tot-Drift
> -------------------------------------------------------------------------------
>
> Potential                   -273047    626.559    611.258  -0.305998
> -476.731
> Total-Energy                -184656    839.662    828.307  -0.305999
> -476.731
> *************************************************************************************
>
>
> 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 step.
>
> 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 acceptable."

This book was written nearly 20 years ago, so take with a "grain of
salt" its advice on "general acceptability".

Was this a simple Lennard-Jones system? If not, you are comparing apples
and oranges anyway.

> 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?

kJ/mol per molecule? :-P

The conversion is straightforward, but you may find it easier
conceptually to convert your other sources into kJ/mol.

Mark

```