g_energy computes zero energy values with GPU - Redmine #1727
Archive from user: shruti matix
Using gromacs 5.0.4 on ubuntu 14.04LTS with a GTX 780 graphics card.
After running protein-ligand simulation for 5ns, the log file incorrectly has zero energy values for all other interactions besides protein-protein interaction energy. Therefore, g_energy computes zero energy, if the MD simulation is run on GPU. For example protein-sol, protein-ligand terms are reported as zero. Sample of log file after 5ns, when run on GPU:
Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14
Protein-Protein –5.34952e+05 5.87772e+04 2.24001e+04 1.97106e+03
Protein-LIG 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Protein-SOL 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Protein-rest 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
LIG-LIG 0.00000e+00 0.00000e+00 –2.31495e+02 9.36822e+01
LIG-SOL 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
LIG-rest 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
SOL-SOL 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
SOL-rest 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
rest-rest 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Also, creating index groups and recalculating energies gives the same result (i.e 0 energy values).
However, energy values with CPU compute alone are reported correctly as follows:
Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14
Protein-Protein –3.71234e+04 –3.56640e+03 2.23658e+04 1.96863e+03
Protein-LIG –4.83560e+01 –1.60406e+02 0.00000e+00 0.00000e+00
Protein-SOL –1.22081e+04 –9.70665e+02 0.00000e+00 0.00000e+00
Protein-rest –2.45000e+02 4.48613e+00 0.00000e+00 0.00000e+00
LIG-LIG 1.22436e+02 –1.21079e+01 –2.31954e+02 9.38064e+01
LIG-SOL –3.28865e+01 –3.46725e+01 0.00000e+00 0.00000e+00
LIG-rest –2.87743e-02 –4.00634e-02 0.00000e+00 0.00000e+00
SOL-SOL –4.48286e+05 6.08941e+04 0.00000e+00 0.00000e+00
SOL-rest –2.49492e+04 2.54938e+03 0.00000e+00 0.00000e+00
rest-rest –1.20356e+04 8.39394e+01 0.00000e+00 0.00000e+00
T-Protein T-non-Protein
2.99899e+02 3.00003e+02
Might be same issue as http://redmine.gromacs.org/issues/1293 (not sure)
(from redmine: issue id 1727, created on 2015-05-06 by gmxdefault, closed on 2015-05-06)
- Relations:
- relates #1822 (closed)
- duplicates #1293 (closed)