Documentation/Nodes/Molecular Dynamics

Molecular Dynamics Nodes

Complete GROMACS integration for molecular dynamics simulations, from system preparation to production runs and comprehensive trajectory analysis.

Node Reference

Comprehensive documentation for GROMACS molecular dynamics nodes in Bioshift.

GROMACS Preparation

Prepare TPR file using MDP parameters, structure, and topology for GROMACS simulation

Type: gromacs_prepCategory: System Setup

Key Features

•TPR file generation with grompp
•GPU acceleration support
•Multi-threading configuration
•Version-specific compatibility
•Input validation and error checking
•Automatic file path resolution

Input Ports

input_filefile

Input structure file (.gro/.g96)

topology_filefile

System topology (.top/.tpr/.itp)

mdp_filefile

MDP parameter file

Output Ports

tpr_filefile

Portable run input file (.tpr)

Properties

Property	Type	Default	Description
input_file	string		Input structure file path
topology_file	string		Topology file path
mdp_file	string		MDP parameter file path
gromacs_version	string	2025.1	GROMACS version to use
use_gpu	bool	false	Enable GPU acceleration
threads	int	0	Number of threads (0 = auto)
deffnm	string	run	Default filename stem

GROMACS Minimize

Energy minimization for CHARMM-GUI workflow using optimized GPU settings

Type: gromacs_minimizeCategory: Energy Minimization

Key Features

•Optimized for GPU acceleration
•CHARMM-GUI workflow integration
•Automatic grompp and mdrun execution
•Comprehensive output file generation
•Warning threshold configuration
•Session-based temporary workspace

Input Ports

gro_filefile

Input structure file (.gro)

top_filefile

System topology (.top)

mdp_filefile

MDP parameter file

index_filefile

Optional index file

Output Ports

gro_filefile

Minimized structure (.gro)

log_filefile

Minimization log

tpr_filefile

Run input file (.tpr)

edr_filefile

Energy data (.edr)

Properties

Property	Type	Default	Description
gromacs_version	string	2025.1	GROMACS version to use
use_gpu	bool	true	Enable GPU acceleration
maxwarn	int	1	Maximum warnings allowed

GROMACS Equilibrate

NVT and NPT equilibration with position restraints for membrane proteins

Type: gromacs_equilibrateCategory: Equilibration

Key Features

•Optimized for membrane protein equilibration
•Position restraint support for stability
•GPU-accelerated simulation
•Automatic grompp and mdrun execution
•Checkpoint file generation for continuation
•Comprehensive output file management

Input Ports

gro_filefile

Input structure (.gro)

top_filefile

System topology (.top)

mdp_filefile

MDP parameter file

index_filefile

Optional index file

Output Ports

gro_filefile

Equilibrated structure (.gro)

log_filefile

Equilibration log

tpr_filefile

Run input file (.tpr)

edr_filefile

Energy data (.edr)

cpt_filefile

Checkpoint file (.cpt)

Properties

Property	Type	Default	Description
gromacs_version	string	2025.1	GROMACS version to use
use_gpu	bool	true	Enable GPU acceleration
maxwarn	int	1	Maximum warnings allowed

GROMACS Production

Production MD simulation with trajectory output and performance optimization

Type: gromacs_productionCategory: Production MD

Key Features

•Long-timescale MD production runs
•Checkpoint/restart capability
•GPU-accelerated performance
•Trajectory file generation (.xtc)
•Energy data collection (.edr)
•Automatic grompp and mdrun execution
•Session-based workspace management

Input Ports

gro_filefile

Input structure (.gro)

top_filefile

System topology (.top)

mdp_filefile

MDP parameter file

index_filefile

Optional index file

cpt_filefile

Optional checkpoint for continuation

Output Ports

gro_filefile

Final structure (.gro)

log_filefile

Production log

tpr_filefile

Run input file (.tpr)

edr_filefile

Energy data (.edr)

cpt_filefile

Final checkpoint (.cpt)

xtc_filefile

Trajectory file (.xtc)

Properties

Property	Type	Default	Description
gromacs_version	string	2025.1	GROMACS version to use
use_gpu	bool	true	Enable GPU acceleration
nsteps	int	250000	Number of simulation steps (1ns with dt=0.004)
maxwarn	int	1	Maximum warnings allowed

MDAnalysis

Comprehensive trajectory analysis (RMSD, RMSF, Rg, etc.)

Type: gromacs_analysisCategory: Analysis

Key Features

•RMSD calculation and alignment
•Per-residue RMSF analysis
•Radius of gyration tracking
•Native contact analysis
•Secondary structure evolution

Input Ports

trajectory_filefile

MD trajectory (.xtc/.trr)

topology_filefile

System topology

reference_structurefile

Reference for RMSD

Output Ports

rmsd_datadata

RMSD time series

rmsf_datadata

RMSF per residue

rg_datadata

Radius of gyration

contacts_datadata

Contact analysis

analysis_plotsimage

Analysis visualizations

Properties

Property	Type	Default	Description
selection	string	protein	Atom selection
rmsd_selection	string	backbone	RMSD selection
rmsf_selection	string	name CA	RMSF selection
start_time	float	0	Analysis start (ps)
end_time	float	-1	Analysis end (ps)
stride	int	1	Frame stride

CHARMM-GUI Input

Import and process CHARMM-GUI generated systems

Type: charmm_gui_inputCategory: System Setup

Key Features

•Automatic archive extraction
•Multi-component system support
•Lipid bilayer systems
•Glycosylation support
•Parameter conversion

Input Ports

charmm_archivefile

CHARMM-GUI archive (.tgz)

system_folderfolder

Or extracted folder

Output Ports

gromacs_filesfile

GROMACS input files

topology_filefile

System topology

structure_filefile

Initial structure

mdp_filesfile

MDP parameter files

Properties

Property	Type	Default	Description
system_type	string	auto	System type detection
extract_lipids	bool	true	Extract lipid parameters
convert_topology	bool	true	Convert to GROMACS format

GROMACS Input Editor

Edit and customize MDP parameter files

Type: gromacs_input_editorCategory: Utilities

Key Features

•Template-based editing
•Parameter validation
•Preset configurations
•Batch parameter updates
•Syntax checking

Input Ports

mdp_templatefile

Template MDP file

parameter_dictdata

Parameter modifications

Output Ports

mdp_filefile

Modified MDP file

parametersdata

Parameter dictionary

Properties

Property	Type	Default	Description
simulation_type	string	production	Simulation type preset
integrator	string	md	Integration algorithm
constraints	string	h-bonds	Constraint algorithm
cutoff_scheme	string	Verlet	Neighbor searching

XTC Extractor

Extract frames and reduce trajectory size

Type: xtc_extractorCategory: Trajectory Tools

Key Features

•Time-based extraction
•Frame skipping/striding
•Atom group selection
•PBC correction
•Trajectory centering

Input Ports

trajectory_filefile

Input trajectory

topology_filefile

System topology

index_filefile

Optional index groups

Output Ports

extracted_trajectoryfile

Extracted trajectory

frame_structuresfile

Individual frames

trajectory_infodata

Trajectory metadata

Properties

Property	Type	Default	Description
start_time	float	0	Start time (ps)
end_time	float	-1	End time (ps)
dt	float	100	Output interval (ps)
selection	string	System	Atom group
center	bool	true	Center molecules
pbc	string	mol	PBC treatment

GROMACS Plotting

Plot energy, temperature, pressure from EDR files

Type: gromacs_plotingCategory: Analysis

Key Features

•Energy term extraction
•Temperature/pressure monitoring
•Running averages
•Distribution plots
•Convergence analysis

Input Ports

energy_filefile

Energy file (.edr)

xvg_filesfile

XVG data files

Output Ports

energy_plotsimage

Energy plots

property_datadata

Extracted properties

statisticsdata

Statistical analysis

Properties

Property	Type	Default	Description
properties	string	Potential,Temperature,Pressure	Properties to extract
plot_type	string	time_series	Plot type
running_average	int	10	Running average window

GROMACS Viewer

Interactive 3D trajectory visualization with NGL.js

Type: gromacs_viewerCategory: Visualization

Key Features

•Interactive trajectory playback
•Multiple representations
•Custom color schemes
•Snapshot generation
•Web-based viewer export

Input Ports

trajectory_filefile

MD trajectory

structure_filefile

Structure file

Output Ports

viewer_htmlfile

Interactive viewer HTML

snapshotsimage

Trajectory snapshots

Properties

Property	Type	Default	Description
representation	string	cartoon	Molecular representation
color_scheme	string	chainid	Coloring scheme
show_water	bool	false	Show water molecules
show_ions	bool	true	Show ions

Workflow Examples

Common molecular dynamics workflows you can build with these nodes.

Basic Protein MD Simulation

Standard protein simulation workflow

1Load protein PDB with File Input
2Prepare system with GROMACS Preparation
3Minimize energy with GROMACS Minimize
4Equilibrate with GROMACS Equilibrate (NVT/NPT)
5Run production with GROMACS Production
6Analyze with MDAnalysis
7Visualize with GROMACS Viewer

Protein-Ligand Complex MD

Simulate protein with bound ligand

1Prepare protein and ligand separately
2Generate ligand topology (external)
3Combine with GROMACS Preparation
4Add restraints for equilibration
5Run standard MD protocol
6Analyze binding stability
7Calculate interaction energies

Membrane Protein Simulation

Using CHARMM-GUI prepared system

1Import CHARMM-GUI archive
2Extract GROMACS files
3Run membrane equilibration protocol
4Extended production run
5Analyze lipid properties
6Track protein-membrane interactions
7Calculate membrane thickness