Latest GROMACS Installation
Install and verify GROMACS using an appropriate CPU, CUDA GPU, thread-MPI, or external-MPI pathway.
Compiler and CMakeGPU accelerationMPI planningRegression tests
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GROMACS Tutorials, Rebuilt for Premium Learning
A clean, structured presentation of the uploaded GROMACS tutorial suite by Justin A. Lemkul, with the original tutorial sequence, scientific scope, source links, and attribution preserved.
3Fundamental tutorial pathways
6Advanced and specialized topics
CC-BY 4.0Original tutorial content is attributed to Justin A. Lemkul and the source tutorial page.
Prepare Before Entering the Tutorial Suite
AMRA-Lab places installation and file preparation first so learners enter the original tutorials with a verified setup and organized simulation inputs.
Simulation File Preparation
Inspect, clean, organize, and validate structures, topologies, force-field files, MDP files, index groups, and restraints.
PDB inspectionForce fieldsTopology hierarchyFolder protocol
AMRA-Lab module page coming later →
Complete GROMACS Tutorial Collection
Filter the premium cards by level. Each available card opens the original tutorial source in a new tab.
Important Post-Simulation & Enhanced-Sampling Analyses
A focused post-MD, enhanced-sampling, energetic, secondary-structure, and predictive-modeling pathway covering trajectory quality, protein–ligand retention, DSSP, per-residue energetics, steered molecular dynamics, PMF, QSAR, and publication-oriented interpretation.
1. Prepare the Trajectory
Correct periodic boundaries, center the system, fit the protein, and validate frames.
2. Confirm Stability
Evaluate global structure, residue flexibility, compactness, exposure, and secondary structure.
3. Examine Binding
Track ligand retention, hydrogen bonds, contact occupancy, and energetic contributions.
4. Interpret Dynamics
Use PCA, free-energy landscapes, clustering, and correlation analyses for deeper conclusions.
5. SMD & PMF
Interpret pulling force, displacement, reaction-coordinate behavior, and free-energy profiles.
Essential First Step
Trajectory Processing & PBC Correction
Remove periodic-boundary artifacts, center the complex, fit the protein, and generate analysis-ready trajectories.
Detailed module later→
Core Stability
Protein RMSD
Measure global structural deviation, equilibration behavior, persistent drift, and major conformational transitions.
Detailed module later→
Residue Level
Residue RMSF
Identify flexible loops, stabilized binding-site residues, mobile termini, and mutation-sensitive regions.
Detailed module later→
Compactness
Radius of Gyration & SASA
Assess protein compactness, folding consistency, solvent exposure, and ligand-associated changes in accessible surface area.
Detailed module later→
Interaction Stability
Hydrogen-Bond Analysis
Quantify protein–ligand and intraprotein hydrogen bonds, donor–acceptor persistence, distances, and occupancies.
Detailed module later→
Ligand Retention
Ligand RMSD & Binding-Site Retention
Track ligand pose stability after protein fitting and detect rearrangement, partial escape, or complete unbinding.
Detailed module later→
Binding Contacts
Protein–Ligand Contact Occupancy
Measure persistent hydrophobic, ionic, aromatic, water-mediated, and residue-specific interactions across the trajectory.
Detailed module later→
Binding Energetics
MM/PBSA & MM/GBSA
Estimate relative binding energetics, decompose residue contributions, and identify stabilizing or unfavorable interaction regions.
Detailed module later→
Essential Dynamics
PCA & Essential Dynamics
Reduce high-dimensional motion into dominant collective modes and compare conformational sampling between systems.
Detailed module later→
Energy Basins
Free-Energy Landscape
Map low-energy conformational basins, transition regions, metastable states, and representative structures.
Detailed module later→
Representative States
Clustering & Representative Structures
Group related conformations, calculate cluster occupancy, select medoids, and identify dominant structural states.
Detailed module later→
Correlated Motion
DCCM & Dynamic Network Analysis
Reveal correlated and anticorrelated residue motions, communication pathways, communities, and potential allosteric routes.
Detailed module later→
Enhanced Sampling
Steered Molecular Dynamics Simulation
Apply a controlled pulling force along a defined reaction coordinate to investigate ligand dissociation, molecular separation, or conformational transitions.
Detailed SMD module later→
Pulling Response
Force vs Time Graph
Plot the instantaneous pulling force across simulation time to identify rupture events, peak force, resistance regions, and noisy transitions.
Detailed graph module later→
Free-Energy Profile
Potential of Mean Force Analysis
Construct and interpret a PMF profile from umbrella-sampling windows using WHAM, histogram overlap, convergence checks, and uncertainty estimation.
Detailed PMF module later→
Secondary Structure
DSSP Secondary-Structure Analysis
Monitor time-dependent changes in α-helices, β-sheets, turns, bends, coils, and other secondary-structure assignments throughout the trajectory.
Detailed DSSP module later→
Residue Energetics
Per-Residue Energy Decomposition
Decompose MM/PBSA or MM/GBSA binding energy into residue-level contributions to identify stabilizing hotspots, unfavorable residues, and mutation targets.
Detailed decomposition module later→
Predictive Modeling
QSAR Analysis
Relate molecular descriptors and structural features to biological activity using validated statistical or machine-learning models for compound prioritization.
Detailed QSAR module later→
Recommended order:
Always complete trajectory processing and core stability analyses before advanced PCA, FEL, clustering, network, or binding-energy interpretation. For enhanced sampling, use SMD to generate and inspect the pulling pathway, then prepare umbrella-sampling windows before calculating a PMF with WHAM. Each future module can include exact GROMACS commands, input files, expected plots, troubleshooting, figure captions, Methods text, and manuscript-ready Results guidance. DSSP should be interpreted alongside RMSD and RMSF, per-residue decomposition should follow a validated MM/PBSA or MM/GBSA workflow, and QSAR should use an independently validated dataset, model, and applicability domain.
About the Original Tutorial Suite
The scientific intent, version notes, authorship, paper citation, and usage conditions from the uploaded source page remain visible.
Scientific Scope
The tutorials introduce GROMACS through a typical solvated protein, membrane systems, protein–ligand complexes, free-energy transformations, umbrella sampling, biphasic systems, and virtual sites. The original page describes GROMACS as free, open-source, and one of the fastest molecular-dynamics packages available.
The uploaded source notes that the tutorials assume GROMACS 2018 or newer, while some
updated pathways require version 2025. Using a different version may produce commands,
defaults, or outputs that do not behave exactly as shown.
Author & Citation
Original tutorials: Justin A. Lemkul, Ph.D., Associate Professor, Virginia Tech Department of Biochemistry.
J. A. Lemkul (2018), “From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package, v1.0.”
Move from tutorial practice to guided research execution
AMRA-Lab can later connect each tutorial card to a structured premium lesson page with exact commands, reusable files, troubleshooting, analysis, and publication guidance.
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