Production Molecular Dynamics

Here, we’ll run production molecular dynamics on a protein-ligand complex. To check the available production CLIs, type bss_production and hit tab:

bss_production_gromacs     bss_production_pmemd       bss_production_pmemd_cuda  bss_production_sander      bss_production_somd

We’ll pick gromacs. To check the available arguments and defaults, run

bss_production_gromacs -h

We’ll run a quick 0.1 ns of production molecular dynamics on the protein-ligand complex included with maize-biosimspace for testing. We’ll specify the output name to be gmx_md_out and we’ll save all of the intermediate files (including input scripts, logs, and trajectory files) to a subdirectory in the current working directory by specifying --dump_to .

mkdir gmx_md_example
cd gmx_md_example
cp ../tests/data/complex.* .
bss_production_gromacs --inp complex.prm7 complex.rst7 --runtime 0.1 --save_name gmx_md_out --dump_to .

You should now have the final coordinate file, gmx_md_out.rst7, a copy of the input topology file gmx_md_out.prm7, and a sub-directory containing all of the intermediate files. Note that despite running through GROMACS, we were able to pass in AMBER files as input. This is because BioSimSpace automatically converts between file formats (using Sire under the hood).