1.5 NEMAT Commands

Usage: nemat <command> [options]

Command	Description	Use example
start	Prepare current empty directory for a NEMAT run. Creates default input.yaml and empty folders for ligands and proteins along with default mdppath and membrane.	setup
prep	Assembles the system.	Preparation
prep_<step>	Prepare input files for a specific step (min, eq, md, ti).	Preparation
check_<step>	Checks logs/step.err for GROMACS errors for step (prep, min, eq, md, ti, analyze).	Checking
run_<step>	Submits job array to run the corresponding step (min, eq, md, ti).	Execution
s_<step>	Verifies whether the GROMACS run was successful for step (min, eq, md, ti).	Checking
analyze	Analyzes results and produces plots.	Analysis
img	Generates result images from existing results_summary.csv files.	Analysis
val	Displays validation overlap checks from the analysis log.	Analysis
new	Creates a new run by removing previous input and working files (confirmation prompted).	Other features
copy	Copies the current workpath into a new directory. Useful when reusing dynamics with different transitions. Prompts for destination and copy level (eq, md, all).	Other features
update	Updates NEMAT parameters in current directory to match input.yaml.	Other features
clean	Cleans backup files inside the workPath (confirmation prompted).	Other features
wf	Displays a workflow (wf) of a typical NEMAT run and signals where are you at. If you are rerunning some steps, this will not display the actual current step.	Other features
help	Displays the help message.