Energy minimization using only CPU (GPU not used) — GROMACS 2025.3 version used on Ubuntu

User discussions
1

GROMACS version: Gromacs 2025.3
GROMACS modification: No
Hello,

I am running energy minimization using:

gmx mdrun -v -deffnm em

I am using GROMACS 2025.3 on Ubuntu.
My system has two GPUs installed and they are visible in nvidia-smi.

However, when I run the above command, it runs only on CPU and is very slow.
I expected it to use GPU acceleration.

I also tried running with:

gmx mdrun -deffnm em -nb gpu -pme gpu

but I get this error:

Inconsistency in user input:

Cannot compute PME interactions on a GPU, because:

PME GPU does not support: Non-dynamical integrator (use md, sd, etc)

And in the normal run, I see:

GPU halo exchange will not be activated because:

Energy minimization is not supported.

I am confused — why does energy minimization not use GPUs even though they are detected for other runs?
Could anyone clarify if EM can be accelerated on GPU in GROMACS, and if not, what is the best way to speed it up?

I use a big protein with 1987 amino acids, hence the water box is also big. I also attach a topology information here along with other em executed errors.

Thank you in advance.

2

Energy minimization isn’t supported on GPU. Normally these calculations do not take very long if parallelized across several CPU cores. For a large system, you will need a larger number of CPUs to speed up the process reasonably.