Ana gmx

Command: trjconv

Introduction

Processes trajectory files using GROMACS trjconv to center the system and handle periodic boundary conditions (PBC). This command automates trajectory alignment for structural analysis across multiple directories.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories containing trajectory files to process.
`-n`	`--main-name`	str	`'md.tpr'`	Filename pattern for topology/input files (e.g., `md.tpr`).
`-g`	`--groups`	str (+)	`['1','0']`	Atom groups used by `trjconv` for alignment.
`-ndx`	`--index`	str	`None`	Index file name in each sub-directory, such as tc_index.ndx.
	`-pbc`	str	`'mol'`	PBC treatment method (`mol`, `atom`, `res`, `whole`, `cluster`, `nojump`).
	`-ur`	str	`'compact'`	Unit-cell representation (`rect`, `tric`, `compact`).
`-nw`	`--n-workers`	int	`1`	Number of parallel workers for processing.
`-F`	`--force`	flag	`False`	Reprocess trajectories even if output exists.
`-D`	`--delete`	flag	`False`	Delete existing output files before reprocessing.

Behavior

Locates Files: Searches for main-name.tpr in each directory.
Skips Existing: Ignores directories where *_center.xtc exists (unless --force/--delete is used).
Runs trjconv: Executes with parameters -center, -pbc, and -ur. Users are prompted interactively for group selections.
Parallel Processing: Runs tasks concurrently using n-workers.

Notes

Output file: <main-name>_center.xtc.
Requires GROMACS.
Works with .tpr topology files and .xtc trajectories.

Example

lazydock-cli trjconv -d /path/to/trajectories -n md -g 1 0 -pbc mol -ur compact -nw 4 -F

Command: make_ndx

Introduction

Creates or updates index files for trajectory analysis using GROMACS make_ndx. Specifies atom groups (e.g., protein/ligand) for focused analysis.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories containing topology files.
`-f`	`--main-name`	str	`'md.tpr'`	Filename pattern for topology files.
`-g`	`--groups`	str (+)	`['1','0']`	Groups to include in the index file.
`-o`	`--output`	str	`'ana_index.ndx'`	Name for the output index file.
`-n`	`--index`	str	`None`	Index file name in each sub-directory, such as tc_index.ndx.
`-F`	`--force`	flag	`False`	Overwrite existing index files.
`-D`	`--delete`	flag	`False`	Delete existing index files first.

Behavior

Locates Files: Finds main-name.tpr in each directory.
Skipping: Skips processing if output exists (unless --force/--delete used).
Runs make_ndx: Adds specified groups to the index file. Automatically exits after group selection.

Notes

Requires topology files (.tpr).
Output: <output>.ndx.

Example

lazydock-cli make_ndx -d /path/to/data -f md -g "Protein" "Ligand" -o complex.ndx

Command: simple

Introduction

Performs standard MD analyses (RMSD, RMSF, Rg, Hbonds, SASA, PCA/DSSP) and plots results. Automates common GROMACS tools and visualization.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories to analyze.
`-n`	`--main-name`	str	`'md.tpr'`	Topology filename pattern.
`-t`	`--main-type`	str (+)	`[]`	Additional file type filters.
`-ndx`	`--index`	str	`None`	Input index file (e.g., `ana_index.ndx`).
	`--methods`	str (+)	`[all]`	Analyses to run: `rms`, `rmsf`, `gyrate`, `hbond`, `sasa`, `covar`, `dssp`, `FEL`, `PDF`.
	`--dit-style`	str	`None`	Path to `.mplstyle` file for plot customization.
`-rg`	`--rms-group`	str	`'4'`	Atom group for RMSD/RMSF/Rg calculations.
`-hg`	`--hbond-group`	int (+)	`[1,1]`	Groups for Hbond analysis.
`-sg`	`--sasa-group`	str	`'4'`	Group for SASA calculation.
`-eg`	`--eigenval-group`	str	`'4'`	Group for PCA.
`-dg`	`--dssp-group`	str	`'1'`	Group for DSSP secondary structure.
	`--dssp-num`	flag	`False`	Calculate DSSP residue types.
	`--dssp-clear`	flag	`False`	Clear DSSP selections.
`-xmax`	`--eigenval-xmax`	int	`15`	Maximum value for eigenval plot.
`-F`	`--force`	flag	`False`	Reprocess existing data.
`-D`	`--delete`	flag	`False`	Delete existing results.
	`--task-suffix`	str	`''`	Suffix for task identification.

Behavior

Runs Analysis: Executes tools like rms, rmsf, hbond, etc., per methods list.
Generates Plots: Uses dit for visualization. Plots include RMSD, FEL, and PDFs.
Handles Skips: Ignores tasks where output exists unless -F/-D is specified.

Notes

Requires *_center.xtc (preprocessed by trjconv).
FEL: Free-energy landscape via MD-DaVis.
PDF: Probability density function for RMSD/Rg.

Example

lazydock-cli simple -d /md_runs --methods rms gyrate FEL --hbond-group 1 1 -F

Command: mmpbsa

Introduction

Calculates binding free energies using the MMPBSA method with gmx_MMPBSA. Defines receptor/ligand groups and runs calculations.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories containing simulation files.
`-i`	`--input`	str	Required	MMPBSA config file (e.g., `mmpbsa.in`).
`-o`	`--output`	str	`'MMPBSA_FINAL_RESULTS'`	Output prefix for results.
`-np`	`--np`	int	Required	Number of MPI processes for `gmx_MMPBSA`.
`-top`	`--top-name`	str	`'md.tpr'`	Topology filename pattern.
`-traj`	`--traj-name`	str	`'md_center.xtc'`	Trajectory filename pattern.
	`--receptor-chain-name`	str	Required	Receptor chain ID (e.g., `"A"`).
	`--ligand-chain-name`	str	Required	Ligand chain ID (e.g., `"LIG"`).
`-F`	`--force`	flag	`False`	Reprocess even if output exists.

Behavior

Defines Groups: Automatically extracts receptor/ligand atom ranges from topology.
Creates Index: Generates mmpbsa.ndx with receptor/ligand groups.
Runs MMPBSA: Executes gmx_MMPBSA with MPI (-np) on trajectories.

Notes

Requires gmx_MMPBSA installation and *_center.xtc.
Output: <output>.dat (energies) and <output>.csv.

Example

lazydock-cli mmpbsa -d /binding_sims -i mmpbsa.in -np 8 --receptor-chain-name A --ligand-chain-name LIG

Command: interaction

Introduction

Identifies non-covalent interactions (e.g., H-bonds, hydrophobic) between receptor and ligand across frames. Supports PyMOL and PLIP.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories to analyze.
`-gro`	`--gro-name`	str	`'md.gro'`	Structure file (.gro).
	`--alter-receptor-chain`	str	`None`	Override receptor chain ID.
	`--alter-ligand-chain`	str	`None`	Override ligand chain ID.
	`--alter-ligand-res`	str	`None`	Override ligand residue name.
	`--alter-ligand-atm`	str	`None`	Override ligand atom type.
	`--method`	str	`'pymol'`	Tool: `pymol` or `plip`.
	`--mode`	str	`'all'`	Interaction types (comma-separated).
	`--cutoff`	float	`4.0`	Distance threshold (Å).
	`--hydrogen-atom-only`	flag	`False`	Only analyze polar contacts.
	`--output-style`	str	`'receptor'`	Output table format.
	`--max-plot`	int	`None`	Maximum residues to plot.
	`--skip-plot`	flag	`False`	Skip plot generation.
	`--ref-res`	str	`''`	Reference residue names.
`-nw`	`--n-workers`	int	`4`	Number of parallel processes.
`-b`	`--begin-frame`	int	`1`	First frame to analyze.
`-e`	`--end-frame`	int	`None`	Last frame to analyze.
`-step`	`--traj-step`	int	`1`	Step while reading trajectory.
	`--plot-time-unit`	int	`100`	Frames per heatmap time unit.
	`--yticks-interval`	int	`10`	Interval for y axis ticks.
	`--fig-size`	int (+)	`[9, 6]`	Figure size.

Behavior

Maps Interactions: Per-frame detection using PyMOL/PLIP and stores results.
Filters/Plots: Generates residue-level heatmaps showing interaction frequencies.
Parallelizes: Frame processing distributed across workers.

Notes

Output: CSV tables and heatmap plots (*_interactions.png).
Use --alter-* if topology chain IDs mismatch expectations.

Example

lazydock-cli interaction -d /complexes --method plip --mode all --cutoff 5.0 --nw 8

Command: rrcs

Introduction

Computes Residue-Residue Contact Scores (RRCS) to quantify dynamic interactions within chains across frames. Generates heatmaps and line plots.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories to analyze.
`-top`	`--top-name`	str	`'md.tpr'`	Topology filename pattern.
`-gro`	`--gro-name`	str	`'md.gro'`	Structure file (.gro).
`-traj`	`--traj-name`	str	`'md_center.xtc'`	Trajectory filename pattern.
`-c`	`--chains`	str (+)	`None`	Chains to analyze (e.g., `A`, `B`).
`-np`	`--n-workers`	int	`4`	Parallel worker count.
`-b`	`--begin-frame`	int	`0`	First frame to process.
`-e`	`--end-frame`	int	`None`	Last frame to process.
`-step`	`--traj-step`	int	`1`	Step while reading trajectory.
	`--backend`	str	`'numpy'`	Compute backend: `numpy`, `torch`, or `cuda`.

Behavior

Calculates RRCS: Per-frame residue pair scoring.
Aggregates & Plots: Generates three plots:
Average heatmap of RRCS.
Diagonal RRCS values vs. frame.
Line plots for top-scoring residue pairs.
Fast Backends: GPU acceleration via PyTorch (--backend cuda).

Notes

Output: .npz file with scores and PNG plots.

Example

lazydock-cli rrcs -d /dynamics --chains A B --nw 4 --backend cuda

Command: porcupine

Introduction

Generates PyMOL "porcupine plots" using modevectors to visualize structural dynamics. Shows displacement vectors between start/end states.

Parameters

Short	Long	Type	Default	Description
`-d`	`--batch-dir`	str (+)	`['.']`	Directories to analyze.
`-top`	`--top-name`	str	`'md.tpr'`	Topology filename pattern.
`-traj`	`--traj-name`	str	`'md_center.xtc'`	Trajectory filename pattern.
`-b`	`--begin-frame`	int	`0`	First frame.
`-e`	`--end-frame`	int	`None`	Last frame.
`-step`	`--traj-step`	int	`1`	Step while reading trajectory.
`-nw`	`--n-workers`	int	`4`	Number of parallel processes.
`-F`	`--force`	flag	`False`	Reprocess even if output exists.
`-D`	`--delete`	flag	`False`	Delete existing output.

Behavior

Loads Trajectory: Splits into start/end states.
Calculates Vectors: Runs modevectors to generate displacements.
Saves Session: Exports .pse file for PyMOL.

Notes

Requires PyMOL and MDAnalysis.
Output: <traj>_porcupine.pse.

Example

lazydock-cli porcupine -d /motions -b 0 -e 1000