I’ve used the Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
–AmberTools package version–
following the instructions:
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
conda env create -f conda_env/environment.yml
conda activate biobb_AMBER_MDsetup_tutorials
I have also installed AmberTools23 and Amber22 on the same system ( UBUNTU 22.04 ) compiling both from the sources with -DCUDA=TRUE -DOPENMP=TRUE.
It is possible to run the notebook using the sander and pmemd that have been compiled from the
sources so to use all threads and the gpu?
I have run the notebook and analyzing htop I have noticed that only one thread has been used during all the processing and I guess that the gpu was never used.