[gmx-users] OpenMM

[Mark Abraham]

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