Ok...so how could I know the energies among atoms? And how
can I test if my parallel code is running in the correct
manner?
Thanks,
Giulia
On Wed, 14 Apr 2010 16:43:13 +1000
Mark Abraham <mark.abra...@anu.edu.au> wrote:
On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote:
Hi,
thanks a lot for your answer, but I have some doubts
yet...
My .gro files are very different and I'm not sure that
the architecture
(CPU / GPU) could influence the result so much as in my
example (the
first is the output of the serial code and the second
that of the
parallel ones).
MD is chaotic. Tiny differences at an early stage lead
to wildly different results later. That's inevitable.
However ensemble averages should converge to the same
value.
SERIAL CODE:
1LYSH N 1 3.240 2.123 0.830 0.0828 0.7601 -0.2788
1LYSH CA 2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660
1LYSH CB 3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772
1LYSH CG 4 3.103 2.403 0.867 -1.1970 0.3922 0.0170
1LYSH CD 5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267
1LYSH CE 6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567
1LYSH NZ 7 3.024 2.505 1.220 0.2425 1.4466 -0.1367
1LYSH C 8 3.006 2.065 0.754 0.1697 -0.4396 0.7191
1LYSH O 9 2.896 2.086 0.701 0.0216 -1.3952 0.6269
2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099
2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933
2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277
PARALLEL CODE:
1LYSH N 1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669
1LYSH CA 2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385
1LYSH CB 3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935
1LYSH CG 4 3.219 2.261 0.586 0.0989 -0.2444 0.4520
1LYSH CD 5 3.100 2.352 0.558 0.5215 0.0874 -0.3041
1LYSH CE 6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025
1LYSH NZ 7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084
1LYSH C 8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520
1LYSH O 9 3.007 2.030 0.837 0.2640 0.4243 -0.1313
2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992
2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497
2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684
Then, even if in the .log file (parallel code), the
energy terms are
null at every time step to avoid slow communication
between GPU and CPU,
the average energies are null too. (I have test this
also using g_energy)
AVERAGES:
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00
LJ (SR) Coulomb (SR) RF excl. Potential Kinetic En.
0.00000e+00 0.00000e+00 0.00000e+00 -1.05419e+06
5.24361e+05
Total Energy Temperature Pressure (bar) Cons. rmsd ()
-5.29827e+05 3.39337e+04 0.00000e+00 0.00000e+00
There's no evidence of a problem here, given that
because the GPU version will not report such energies,
there's nothing to average.
Mark
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