On 14/04/2010 7:10 PM, PACIELLO GIULIA wrote:
Well,
I have used the option -rerun to 'rerun' on CPU the simulation from the
parallel code. As you can see in the following tables, results are very
similar for non bonded terms, but not for the other energetic terms
(these are avereges obtained from g_energy):
You haven't done a simulation. You've done an energy minimization.
There's no reason to expect the same result for EM on different machines
because there are so many different minima that might be found, and
small numerical differences might mean you find different ones.
PARALLEL CODE
Angle: 4256.27
Prop-di: 322.302
R-B: 3101.14
LJ-14: 2107.6
Coul-14: 15212
LJ(SR): -3410.22
Coul(SR): -29368.3
RF(excl): -9425.23
Pot.En: -17204.5
Kin.En: 5243.87
Tot.En: -11960.6
SERIAL CODE:
Angle: 6089.56
Prop-di: 466.121
R-B: 3677.95
LJ-14: 2234.85
Coul-14: 15149.8
LJ(SR): -3144
Coul(SR): -29240.7
RF(excl): -9425.25
Pot.En: -14191.7
Kin.En: 8262.96
Tot.En: -5929.78
I can't use the -reprod option, but I have noticed that the .gro files
after the energy minimization are very similar (I have performed this
minimization on the .gro files obtained running the parallel and serial
codes)...systems are converging to the same equilibrium ensamble?
No, they've just done an EM. There's no velocities yet, so they're not
in any ensemble. Equilibrate, and then look at ensemble averages of the
equilibrated systems.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
