Is Sander in the amber wrapper GPU enabled? If yes, on the protein-ligand complex tutorial how do I get it to use GPUs on my workstation?
Hi,
sorry for the late reply.
As far as I know, only pmemd tool (under license) from Amber is prepared to use the GPUs of the machine, sander (free tool) is just compatible with CPUs.
To take advantage of your GPU card, you can either try to obtain an Amber license, or install GROMACS in your machine and (if you want to use BioBB workflows), use the protein-ligand GROMACS workflow changing the gmx_path property to the corresponding locally installed gmx_mpi binary in your system.
We are currently working on a GPU-compatible GROMACS Conda package, so that the BioBB building blocks using GROMACS could directly use the GPU card, but it is still in progress.
Hope it helps!