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):
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?
I'm thankful for your help,
Giulia
On Wed, 14 Apr 2010 18:03:43 +1000
Mark Abraham <[email protected]> wrote:
On 14/04/2010 5:18 PM, PACIELLO GIULIA wrote:
I dont'know if this is the right way to test that things
converge to the
same value...but I have made an energy minimization on
CPU of the two
output (parallel and serial). I have obtained this
results:
FROM PARALLEL OUTPUT
Potential Energy = -1.6960029e+04
Maximum force = 1.7282695e+03 on atom 364
Norm of force = 4.6171844e+02
FROM SERIAL OUTPUT
Potential Energy = -1.7814945e+04
Maximum force = 2.1551072e+03 on atom 496
Norm of force = 2.9537823e+02
They're probably both fine. By "converged" I was
referring to an equilibrium MD ensemble.
Mark
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