GROMACS Molecular Dynamics
Complete GROMACS 2025.1 integration for molecular dynamics simulations, from system preparation to production runs and comprehensive trajectory analysis.
GROMACS Node Reference
Comprehensive molecular dynamics nodes powered by GROMACS 2025.1 with GPU acceleration.
GROMACS Preparation
Generate TPR file for molecular dynamics simulations
Key Features
- •Automatic grompp execution
- •GPU acceleration support
- •Multi-threading optimization
- •Input validation and error checking
- •Session-based temp workspace
- •Version compatibility handling
Input Ports
Structure file (.gro/.g96)
Topology file (.top/.tpr/.itp)
MDP parameter file
Output Ports
Binary run input file (.tpr)
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| gromacs_version | string | 2025.1 | GROMACS version |
| use_gpu | bool | false | Enable GPU acceleration |
| threads | int | 0 | CPU threads (0=auto) |
| deffnm | string | run | Default output file name |
GROMACS Minimize
Energy minimization using steepest descent or conjugate gradient
Key Features
- •GPU-accelerated minimization
- •Automatic convergence detection
- •Energy monitoring and analysis
- •CHARMM-GUI workflow compatible
- •Real-time progress updates
- •Comprehensive output files
Input Ports
Input structure (.gro)
Topology (.top)
Minimization parameters (.mdp)
Optional index file (.ndx)
Output Ports
Minimized structure
Minimization log
Run input file
Energy data
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| gromacs_version | string | 2025.1 | GROMACS version |
| use_gpu | bool | true | Use GPU if available |
| maxwarn | int | 1 | Maximum warnings allowed |
GROMACS Equilibrate
NVT and NPT equilibration with position restraints
Key Features
- •NVT and NPT ensemble support
- •Position restraints for proteins
- •Checkpoint-based continuation
- •Temperature and pressure coupling
- •Membrane protein support
- •Real-time monitoring
Input Ports
Input structure
Topology
Equilibration parameters
Optional index file
Optional checkpoint for continuation
Output Ports
Equilibrated structure
Equilibration log
Run input file
Energy data
Checkpoint file
Full precision trajectory
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| gromacs_version | string | 2025.1 | GROMACS version |
| use_gpu | bool | true | GPU acceleration |
| maxwarn | int | 1 | Maximum warnings |
| checkpoint_interval | int | 15 | Checkpoint interval (minutes) |
GROMACS Production
Production MD runs with advanced sampling options
Key Features
- •Long timescale simulations
- •GPU acceleration for performance
- •Checkpoint-based restart capability
- •XTC trajectory compression
- •Parallel tempering support
- •Enhanced sampling methods
Input Ports
Equilibrated structure
Topology
Production parameters
Optional index file
Checkpoint for continuation
Output Ports
Final structure
Production log
Run input file
Energy data
Final checkpoint
Compressed trajectory
Full precision trajectory
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| gromacs_version | string | 2025.1 | GROMACS version |
| use_gpu | bool | true | GPU acceleration |
| simulation_time | float | 100.0 | Simulation time (ns) |
| nsteps | int | 50000000 | Number of steps |
| checkpoint_interval | int | 15 | Checkpoint interval (minutes) |
MDAnalysis
Trajectory analysis with MDAnalysis toolkit
Key Features
- •RMSD/RMSF calculation
- •Radius of gyration analysis
- •Contact and hydrogen bond analysis
- •Secondary structure tracking
- •Custom atom selections
- •Batch analysis support
Input Ports
Topology file (GRO/TPR/PDB)
Trajectory file (XTC/TRR)
Output Ports
RMSD time series
RMSF per residue
Radius of gyration
Contact analysis
Analysis plots
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| analysis_type | string | rmsd | Type of analysis |
| selection | string | protein | Atom selection |
| start_frame | int | 0 | Starting frame |
| end_frame | int | -1 | Ending frame (-1 for last) |
| step | int | 1 | Frame step |
CHARMM-GUI Input
Import CHARMM-GUI generated system files
Key Features
- •Direct CHARMM-GUI import
- •Membrane protein support
- •Lipid bilayer systems
- •Ion and water handling
- •Force field conversion
- •Automatic file organization
Input Ports
CHARMM-GUI output folder
Output Ports
System structure
System topology
MDP parameter files
Index groups
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| system_type | string | membrane | System type (membrane/solution) |
| force_field | string | charmm36m | Force field version |
GROMACS Input Editor
Edit and customize MDP parameter files
Key Features
- •Interactive MDP editing
- •Parameter validation
- •Template library
- •Ensemble-specific presets
- •Advanced options access
- •Comment preservation
Input Ports
Input MDP file
Output Ports
Modified MDP file
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| integrator | string | md | Integration algorithm |
| dt | float | 0.002 | Time step (ps) |
| nsteps | int | 500000 | Number of steps |
| temperature | float | 300 | Temperature (K) |
| pressure | float | 1.0 | Pressure (bar) |
| tcoupl | string | V-rescale | Temperature coupling |
| pcoupl | string | Parrinello-Rahman | Pressure coupling |
XTC Extractor
Extract frames from compressed trajectories
Key Features
- •Frame extraction by time
- •Custom atom selections
- •Batch frame export
- •PDB format conversion
- •Trajectory subsetting
- •Time series metadata
Input Ports
XTC trajectory file
TPR run input file
Output Ports
Extracted frames as PDB files
Time points of frames
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| start_time | float | 0 | Start time (ps) |
| end_time | float | -1 | End time (ps, -1 for end) |
| dt | float | 100 | Frame interval (ps) |
| selection | string | System | Atom selection |
GROMACS Plotting
Plot energy terms from EDR files
Key Features
- •Energy term extraction
- •Temperature monitoring
- •Pressure tracking
- •Box dimension analysis
- •Interactive plots
- •Export to CSV
Input Ports
Energy data file (.edr)
Output Ports
Energy terms DataFrame
Energy plots
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| terms | string | Potential,Kinetic,Total | Energy terms to extract |
| plot_type | string | line | Plot type (line/scatter) |
| smooth | bool | false | Apply smoothing |
GROMACS Viewer
Interactive trajectory visualization with NGL.js
Key Features
- •Interactive 3D viewer
- •Trajectory playback
- •Multiple representations
- •Custom selections
- •Screenshot export
- •Measurement tools
Input Ports
Structure file (GRO/PDB)
Optional trajectory (XTC/TRR)
Output Ports
Viewer URL
Structure screenshot
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| representation | string | cartoon | Molecular representation |
| color_scheme | string | chainid | Color scheme |
| show_water | bool | false | Show water molecules |
| show_ions | bool | true | Show ions |
Common MD Workflows
Standard molecular dynamics simulation workflows you can build with GROMACS nodes.
Basic Protein Simulation
Standard protein MD workflow
- 1Load protein structure (PDB)
- 2Generate topology with pdb2gmx
- 3Solvate and add ions
- 4Energy minimization
- 5NVT equilibration (100 ps)
- 6NPT equilibration (100 ps)
- 7Production MD (10 ns)
- 8Trajectory analysis
Membrane Protein Simulation
CHARMM-GUI based membrane setup
- 1Import CHARMM-GUI files
- 2Energy minimization (5000 steps)
- 3NVT equilibration with restraints
- 4NPT equilibration (6 steps)
- 5Production MD (100 ns)
- 6Lipid analysis
- 7Protein-lipid contacts
Free Energy Calculation
Alchemical free energy workflow
- 1Setup lambda windows
- 2Equilibrate each window
- 3Production for each lambda
- 4Extract dH/dλ values
- 5MBAR/BAR analysis
- 6Calculate ΔG binding