Energy minimization crashes on GPU but not CPU

User discussions
1

GROMACS version: 2024.4
GROMACS modification: Yes/No

I’m running minimization on GPU. However, the output gro file show the protein is fragmented even there is no error reported during minimization. When I tried again minimization on CPU with the same minimization and input file, the output gro file some protein is intact and there is no fragmentation. I would like to run on GPU to speed up. Can anyone explains me what happens here and how to fix it ? Thanks

2

Hi @nthpham,

I think the problem you are having is a visualization one, try to clean up the trajectory with gmx trjconv. Also I do not think that the minimization can be run on GPU, it’s always on CPU, while dynamics can (and should, as it’s significantly faster).

3

Hi ObZehn,

I try trjconv, it looks good now. You’re right, it’s visualization issue.

Thanks for suggestions !

Hang