[gmx-users] OpenMM

[PACIELLO GIULIA]

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).

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


Thanks in advance,
Giulia

On Tue, 13 Apr 2010 19:14:29 +0200
  Rossen Apostolov <rossen.apostolov at cbr.su.se> wrote:
> Hi,O
> 
> On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote:
>> Even if I have followed all the instructions reported 
>>for the correct installation of GPU, CUDA, OpenMM and 
>>even if my .mdp file for the simulation is written 
>>following the features supported in the release 
>>Gromacs-OpenMM, the output of the serial code running on 
>>CPU is quite different from that of the parallel code 
>>running on GPU (.gro files).
> That is normal. The architectures are different and the 
>algorithms are different so you can't expect numerically 
>identical results. The simulated ensembles should be 
>properly generated though.
>>
>> Looking at the .log file I have also noticed that the 
>>energy terms 'Angle', 'Proper 
>>Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 
>>'Coulomb (SR), 'RF excl', are null for the simulation 
>>performed with the parallel code.
>>
> OpenMM doesn't report individual energy and force terms, 
>only the totals. This is done for efficiency reasons - it 
>saves GPU memory and avoids slow CPU<->GPU transfers.
> 
> Rossen
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