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
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