Command: simple-protein
Introduction
The simple-protein command automates a complete GROMACS simulation workflow for proteins. It performs a series of steps including box creation, solvation, ionization, energy minimization, equilibration, and production molecular dynamics.
Parameters
| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-d |
--batch-dir |
str (+) | ['.'] |
Directories containing protein files to process. |
-n |
--protein-name |
str | Required | Protein filename in each sub-directory (e.g., protein.gro). |
-st |
--start-time |
str | None |
Start time for execution (format: "2025-01-15 17:30:00"). |
--auto-box |
flag | False |
Automatically generate rectangular bounding box using PyMOL. | |
--auto-box-padding |
float | 1.2 |
Padding distance for automatic box generation. | |
--ion-mdp |
str | Required | Ion addition MDP file. | |
--em-mdp |
str | Required | Energy minimization MDP file. | |
--nvt-mdp |
str | Required | NVT equilibration MDP file. | |
--npt-mdp |
str | Required | NPT equilibration MDP file. | |
--md-mdp |
str | Required | Production MD MDP file. | |
--editconf-args |
str | "-c -d 1.2 -bt dodecahedron" |
Arguments for editconf command. | |
--solvate-args |
str | "-cs spc216.gro" |
Arguments for solvate command. | |
--genion-args |
str | "-pname NA -nname CL -neutral" |
Arguments for genion command. | |
--em-args |
str | "" |
Arguments for mdrun during energy minimization. | |
--mdrun-args |
str | "-v -ntomp 4 -update gpu -nb gpu -pme gpu -bonded gpu -pmefft gpu" |
Arguments for production mdrun. | |
--genion-groups |
str | "SOL" |
Group for ion replacement. | |
--potential-groups |
str | "11 0" |
Groups to plot potential energy. | |
--temperature-groups |
str | "16 0" |
Groups to plot temperature. | |
--pressure-groups |
str | "17 0" |
Groups to plot pressure. | |
--density-groups |
str | "23 0" |
Groups to plot density. | |
--maxwarn |
int | 0 |
Maximum warnings for grompp commands. |
Behavior
- Box Creation: Uses
editconfto create a simulation box around the protein - Solvation: Adds water molecules using
solvate - Ionization: Replaces water molecules with ions using
genion - Energy Minimization: Minimizes system energy using steepest descent
- NVT Equilibration: Equilibrates system at constant volume and temperature
- NPT Equilibration: Equilibrates system at constant pressure and temperature
- Production MD: Runs the production molecular dynamics simulation
Notes
- The command automatically generates plots for potential, temperature, pressure, and density
- If
md.tpralready exists in the directory, the simulation is skipped - MDP files are required for each simulation step
- Supports GPU acceleration through mdrun arguments
Example
lazydock-cli run-gmx simple-protein -d /path/to/protein/directory -n protein.gro --ion-mdp ions.mdp --em-mdp em.mdp --nvt-mdp nvt.mdp --npt-mdp npt.mdp --md-mdp md.mdp
Command: simple-ligand
Introduction
The simple-ligand command automates a complete GROMACS simulation workflow for ligands. It follows the same steps as simple-protein but is optimized for small molecule simulations with appropriate default parameters.
Parameters
| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-d |
--batch-dir |
str (+) | ['.'] |
Directories containing ligand files to process. |
-n |
--protein-name |
str | Required | Ligand filename in each sub-directory (e.g., ligand.gro). |
-ln |
--ligand-name |
str | 'lig.gro' |
Ligand filename (used for compatibility with complex workflow). |
-st |
--start-time |
str | None |
Start time for execution (format: "2025-01-15 17:30:00"). |
--auto-box |
flag | False |
Automatically generate rectangular bounding box using PyMOL. | |
--auto-box-padding |
float | 1.2 |
Padding distance for automatic box generation. | |
--ion-mdp |
str | Required | Ion addition MDP file. | |
--em-mdp |
str | Required | Energy minimization MDP file. | |
--nvt-mdp |
str | Required | NVT equilibration MDP file. | |
--npt-mdp |
str | Required | NPT equilibration MDP file. | |
--md-mdp |
str | Required | Production MD MDP file. | |
--editconf-args |
str | "-c -d 1.2 -bt dodecahedron" |
Arguments for editconf command. | |
--solvate-args |
str | "-cs spc216.gro" |
Arguments for solvate command. | |
--genion-args |
str | "-pname NA -nname CL -neutral" |
Arguments for genion command. | |
--em-args |
str | "" |
Arguments for mdrun during energy minimization. | |
--mdrun-args |
str | "-v -ntomp 4 -update gpu -nb gpu -pme gpu -bonded gpu -pmefft gpu" |
Arguments for production mdrun. | |
--genion-groups |
str | "SOL" |
Group for ion replacement. | |
--potential-groups |
str | "10 0" |
Groups to plot potential energy (optimized for ligands). | |
--temperature-groups |
str | "15 0" |
Groups to plot temperature (optimized for ligands). | |
--pressure-groups |
str | "16 0" |
Groups to plot pressure (optimized for ligands). | |
--density-groups |
str | "22 0" |
Groups to plot density (optimized for ligands). | |
--tc-groups |
str | "2" |
Temperature coupling groups for ligand simulations. | |
--maxwarn |
int | 0 |
Maximum warnings for grompp commands. |
Behavior
- Box Creation: Uses
editconfto create a simulation box around the ligand - Solvation: Adds water molecules using
solvate - Ionization: Replaces water molecules with ions using
genion - Energy Minimization: Minimizes system energy using steepest descent
- NVT Equilibration: Equilibrates system at constant volume and temperature
- NPT Equilibration: Equilibrates system at constant pressure and temperature
- Production MD: Runs the production molecular dynamics simulation
Notes
- Uses ligand-optimized default parameters for energy analysis groups
- Temperature coupling groups are set to "2" for ligand simulations
- If
md.tpralready exists in the directory, the simulation is skipped - MDP files are required for each simulation step
- Supports GPU acceleration through mdrun arguments
Example
lazydock-cli run-gmx simple-ligand -d /path/to/ligand/directory -n ligand.gro --ion-mdp ions.mdp --em-mdp em.mdp --nvt-mdp nvt.mdp --npt-mdp npt.mdp --md-mdp md.mdp
Command: simple-complex
Introduction
The simple-complex command automates a complete GROMACS simulation workflow for protein-ligand complexes. It extends the protein workflow with additional steps for handling ligand position restraints and proper temperature coupling groups.
Parameters
| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-d |
--batch-dir |
str (+) | ['.'] |
Directories containing complex files to process. |
-n |
--protein-name |
str | Required | Complex filename in each sub-directory (e.g., complex.gro). |
-ln |
--ligand-name |
str | 'lig.gro' |
Ligand filename in each sub-directory. |
-st |
--start-time |
str | None |
Start time for execution (format: "2025-01-15 17:30:00"). |
--auto-box |
flag | False |
Automatically generate rectangular bounding box using PyMOL. | |
--auto-box-padding |
float | 1.2 |
Padding distance for automatic box generation. | |
--ion-mdp |
str | Required | Ion addition MDP file. | |
--em-mdp |
str | Required | Energy minimization MDP file. | |
--nvt-mdp |
str | Required | NVT equilibration MDP file. | |
--npt-mdp |
str | Required | NPT equilibration MDP file. | |
--md-mdp |
str | Required | Production MD MDP file. | |
--editconf-args |
str | "-c -d 1.2 -bt dodecahedron" |
Arguments for editconf command. | |
--solvate-args |
str | "-cs spc216.gro" |
Arguments for solvate command. | |
--genion-args |
str | "-pname NA -nname CL -neutral" |
Arguments for genion command. | |
--em-args |
str | "" |
Arguments for mdrun during energy minimization. | |
--mdrun-args |
str | "-v -ntomp 4 -update gpu -nb gpu -pme gpu -bonded gpu -pmefft gpu" |
Arguments for production mdrun. | |
--genion-groups |
str | "SOL" |
Group for ion replacement. | |
--potential-groups |
str | "11 0" |
Groups to plot potential energy. | |
--temperature-groups |
str | "16 0" |
Groups to plot temperature. | |
--pressure-groups |
str | "17 0" |
Groups to plot pressure. | |
--density-groups |
str | "23 0" |
Groups to plot density. | |
--lig-posres |
str | 'POSRES' |
Symbol for ligand position restraints. | |
--tc-groups |
str | 'auto' |
Temperature coupling groups (auto-detects Protein and LIG). | |
--maxwarn |
int | 0 |
Maximum warnings for grompp commands. |
Behavior
- Box Creation: Uses
editconfto create a simulation box around the complex - Solvation: Adds water molecules using
solvate - Ionization: Replaces water molecules with ions using
genion - Energy Minimization: Minimizes system energy using steepest descent
- Ligand Restraints: Creates position restraints for the ligand:
- Generates index file for ligand heavy atoms
- Creates position restraint file with force constants of 1000 kJ/mol/nm²
- Inserts restraint information into topology file
- Temperature Coupling Groups: Creates custom temperature coupling groups:
- Automatically detects Protein and LIG groups if set to 'auto'
- Creates index file for proper temperature coupling
- NVT Equilibration: Equilibrates system at constant volume and temperature
- NPT Equilibration: Equilibrates system at constant pressure and temperature
- Production MD: Runs the production molecular dynamics simulation
Notes
- Automatically creates ligand position restraints to prevent unrealistic movements
- Temperature coupling groups are set up to allow different temperatures for protein and ligand
- If
md.tpralready exists in the directory, the simulation is skipped - MDP files are required for each simulation step
- Supports GPU acceleration through mdrun arguments
Example
lazydock-cli run-gmx simple-complex -d /path/to/complex/directory -n complex.gro -ln ligand.gro --ion-mdp ions.mdp --em-mdp em.mdp --nvt-mdp nvt.mdp --npt-mdp npt.mdp --md-mdp md.mdp