The two tables was the averages generated by the serial
code and by the parallel code (I have used, as you suggest
me, the option rerun of mdrun on the CPU to analyze the
energies obtained with the parallel simulation on
GPU)...Could you tell me if these results could be correct
and why?
I have also another question...in a precedent post you
said me that .gro files from serial and parallel codes are
different for two main reasons: the architecture used to
simulate the ensamble and the algorithms implemented.
Could you tell me more about this? If MD is deterministic
which is the correct solution? Which are the
approximations done?
Thanks a lot,
Giulia
On Thu, 15 Apr 2010 08:53:07 +1000
Mark Abraham <mark.abra...@anu.edu.au> wrote:
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 gmx-users@gromacs.org
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
gmx-users-requ...@gromacs.org.
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list gmx-users@gromacs.org
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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
