[gmx-users] question about energy fluctuation

[Mark Abraham]

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