Documentation/Scientific Engines/Molecular Dynamics

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

Type: gromacs_prepCategory: System Setup

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

input_filefile

Structure file (.gro/.g96)

topology_filefile

Topology file (.top/.tpr/.itp)

mdp_filefile

MDP parameter file

Output Ports

tpr_filefile

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

Type: gromacs_minimizeCategory: Energy Minimization

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

gro_filefile

Input structure (.gro)

top_filefile

Topology (.top)

mdp_filefile

Minimization parameters (.mdp)

index_filefile

Optional index file (.ndx)

Output Ports

gro_filefile

Minimized structure

log_filefile

Minimization log

tpr_filefile

Run input file

edr_filefile

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

Type: gromacs_equilibrateCategory: Equilibration

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

gro_filefile

Input structure

top_filefile

Topology

mdp_filefile

Equilibration parameters

index_filefile

Optional index file

cpt_filefile

Optional checkpoint for continuation

Output Ports

gro_filefile

Equilibrated structure

log_filefile

Equilibration log

tpr_filefile

Run input file

edr_filefile

Energy data

cpt_filefile

Checkpoint file

trr_filefile

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

Type: gromacs_productionCategory: MD Simulation

Key Features

•Long timescale simulations
•GPU acceleration for performance
•Checkpoint-based restart capability
•XTC trajectory compression
•Parallel tempering support
•Enhanced sampling methods

Input Ports

gro_filefile

Equilibrated structure

top_filefile

Topology

mdp_filefile

Production parameters

index_filefile

Optional index file

cpt_filefile

Checkpoint for continuation

Output Ports

gro_filefile

Final structure

log_filefile

Production log

tpr_filefile

Run input file

edr_filefile

Energy data

cpt_filefile

Final checkpoint

xtc_filefile

Compressed trajectory

trr_filefile

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

Type: gromacs_analysisCategory: Analysis

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

topologyfile

Topology file (GRO/TPR/PDB)

trajectoryfile

Trajectory file (XTC/TRR)

Output Ports

rmsddata

RMSD time series

rmsfdata

RMSF per residue

rgdata

Radius of gyration

contactsdata

Contact analysis

analysis_plotsimage

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

Type: charmm_gui_inputCategory: System Setup

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_folderfolder

CHARMM-GUI output folder

Output Ports

gro_filefile

System structure

top_filefile

System topology

mdp_fileslist

MDP parameter files

index_filefile

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

Type: gromacs_input_editorCategory: System Setup

Key Features

•Interactive MDP editing
•Parameter validation
•Template library
•Ensemble-specific presets
•Advanced options access
•Comment preservation

Input Ports

mdp_filefile

Input MDP file

Output Ports

mdp_filefile

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

Type: xtc_extractorCategory: Trajectory Tools

Key Features

•Frame extraction by time
•Custom atom selections
•Batch frame export
•PDB format conversion
•Trajectory subsetting
•Time series metadata

Input Ports

xtc_filefile

XTC trajectory file

tpr_filefile

TPR run input file

Output Ports

frameslist

Extracted frames as PDB files

time_seriesdata

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

Type: gromacs_plotingCategory: Analysis

Key Features

•Energy term extraction
•Temperature monitoring
•Pressure tracking
•Box dimension analysis
•Interactive plots
•Export to CSV

Input Ports

edr_filefile

Energy data file (.edr)

Output Ports

energy_datadata

Energy terms DataFrame

plotsimage

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

Type: gromacs_viewerCategory: Visualization

Key Features

•Interactive 3D viewer
•Trajectory playback
•Multiple representations
•Custom selections
•Screenshot export
•Measurement tools

Input Ports

structurefile

Structure file (GRO/PDB)

trajectoryfile

Optional trajectory (XTC/TRR)

Output Ports

viewer_urlstring

Viewer URL

screenshotimage

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