[gmx-users] OpenMM

Rossen Apostolov rossen.apostolov at cbr.su.se
Tue Apr 13 19:14:29 CEST 2010


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.


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