Mark Abraham wrote:
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 book is fine, but limited to LJ systems. Therefore Mark's question
is important.
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.
You can divide by the number of molecules using g_energy -nmol.
The reason GROMACS doesn't do it for you is that it is well defined only
for monomolecular systems. The energy you get is hence kJ/mol system.
Where system is your complete system, be it 125 argon atoms or a large
biological complex.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
