Running Unbinding Kinetics from the Command Line

Unbinding Kinetics is a workflow for sampling both unbinding pathways and absolute residence times. The workflow runs in two stages. First, Random Acceleration Molecular Dynamics (RAMD) is used to sample exit pathways and their relative frequencies. Then, Infrequent Metadynamics is used to sample unbinding events along the most common exit pathway(s) and their associated timescales.

Running Unbinding Kinetics Simulations

Submit the Unbinding Kinetics simulation on the command line:

$SCHRODINGER/unbinding_kinetics input.mae -HOST CpuHost -SUBHOST GpuHost -OPLS_DIR opls_dir -JOBNAME jobname

Some useful options include:

-membrane {None|DMPC|POPE|DPPC|POPC}

Will automatically build the lipid bilayer, input must be OPM-compatible

-asl-ligand

Define ligand ASL, if it cannot be detected automatically

-prepare

Write inputs/protocol files without launching the job, for granular parameter control

-ramd-only

Runs only RAMD part, generating exit pathway cloud

See unbinding_kinetics Command Help for a complete list of options.