[gmx-developers] question about energy fluctuation

[Anton Feenstra]

Qiao Baofu wrote:
> Hi all,
> 
> After running a MD of a system with about 17000 atoms, I calculated the
> potential and the total-energy:
[...]

> 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."
> 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.

I'd guess your 17000 atom-system is not 'a simple L-J system'.
Charges and/or bonds will have a big influence here. There are many
papers around that discuss accuracy of simulations in relation to
energy drift and/or fluctuations. You can check

K. Anton Feenstra, Berk Hess and Herman J. C. Berendsen. Improving 
Efficiency of Large Time-scale Molecular Dynamics Simulations of 
Hydrogen-rich Systems. (1999) J. Comput. Chem. 20 (8), 786-798

and especially the references to A.K. Mazur.

> 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?

I'm not sure what you mean. 'mol' is, basically, Avogadro's number.


-- 
Groetjes,

Anton

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