Version 0.0.3 | Desmond MD ✅ • GROMACS ✅ • LAMMPS ✅
MOTUS is a unified molecular simulation analysis platform that transforms raw MD trajectory data into publication-ready figures and quantitative insights — automatically, across three industry-standard engines.
Molecular dynamics simulations are a cornerstone of modern science and engineering. By tracking every atom's motion at femtosecond resolution, MD reveals the invisible machinery behind:
- ⚡ Energy Storage — electrolyte structure, ion transport mechanisms, and electrode-electrolyte interfaces in next-generation batteries
- 🧬 Drug Discovery — protein-ligand binding free energies, conformational selection, and solvation effects that govern drug efficacy
- 🧪 Catalysis — reaction pathways, transition states, and solvent effects in homogeneous and heterogeneous catalysis
- 🛡️ Materials Design — polymer mechanics, membrane permeability, and self-assembly of functional nanomaterials
- 🌍 Climate & Geochemistry — CO₂ capture solvents, mineral dissolution kinetics, and atmospheric aerosol chemistry
Across all these fields, the bottleneck is the same: turning terabytes of simulation data into interpretable, publication-quality results. MOTUS eliminates this bottleneck.
One command. Three engines. Fifteen analysis types. Zero manual plotting.
# From raw trajectory to complete analysis package — run from within the job folder
cd desmond_md_job_my-system
../motus/desmond/desmond-analysis.sh --plot
# → energy, Hbonds, RDF, density, dipole, clustering, PCA, SIMA...
# → all figures in PDF (vector) + PNG (300 DPI)
# → < 2 minutesNew in v0.0.3: Auto-detect current working directory — no folder paths needed. Just cd into your job folder and run. Supports Maestro output from both Windows (CRLF) and Linux, with automatic line-ending conversion.
Recommended workflow: Set up your system in Maestro (Windows or Linux), write the job files, then run on your GPU server.
# 1. Copy the Maestro-generated folder to your Linux server
# Maestro produces: desmond_md_job_my-system/{.cms, .msj, .cfg}
# 2. Enter the folder and launch MD
cd desmond_md_job_my-system
bash ../motus/desmond/desmond-md.sh # Use Maestro settings as-is
bash ../motus/desmond/desmond-md.sh -t 5000 -i 2.5 # Or override time & interval
# Real-time output: Stage progress + production progress bar
# Stage 1 completed. Stage 2 completed. ...
# [=========-----] 65% | 32500/50000 ps | 2513 ns/day
# 3. Full analysis + figures (same folder)
bash ../motus/desmond/desmond-analysis.sh --plot
# 4. Re-plot from existing data (seconds)
bash ../motus/desmond/desmond-analysis.sh --fig-onlyKey features:
- Windows & Linux Maestro — auto-detects and fixes CRLF line endings (
\r\n→\n) - CWD auto-detection — no folder path needed; just
cdinto the job folder - Real-time progress bar — shows
Chemical time,ns/day, and percentage during MD runs - Dynamic server paths — auto-discovers Schrödinger scratch directory (works across different cluster configurations)
- Stage-by-stage monitoring — shows
_multisim.logoutput during equilibration phases
Legacy mode (--mode 2): Build from a desmond_setup_XXXXX folder (generates .msj and .cfg from CLI parameters):
./desmond/desmond-md.sh --mode 2 desmond_setup_my-system -t 2000 -i 1
### GROMACS
```bash
# MD production run (EM → NVT → NPT → Prod)
./gromacs/gromacs-md.sh my-system.gro my-system.top
# Full analysis + figures
./gromacs/gromacs-analysis.sh md_output/ --plot
# Enhanced sampling
./gromacs/gromacs-metadynamics.sh md_output/
./gromacs/gromacs-umbrella.sh md_output/ -d 0.05 -w 12 -s 0.3# Standard MD production run
./lammps/lammps-md.sh system.data
# Analysis + figures
./lammps/lammps-analysis.sh md_output/
# Enhanced sampling
./lammps/lammps-metadynamics.sh md_output/
# Reactive MD — ReaxFF (high-temperature reaction kinetics)
./lammps/lammps-reaxff.sh system.data -T 2500 -t 500
./lammps/lammps-reaxff-analysis.sh md_output/
# Reactive MD — fix bond/react (template-driven at any temperature)
./lammps/lammps-bond-react.sh system.data -m reaction.yaml -T 400 -t 2000LAMMPS Reaction Kinetics (lammps-reaxff.sh, lammps-bond-react.sh, lammps-reaxff-analysis.sh):
- ReaxFF — reactive force field MD with automatic species tracking; suitable for high-T pyrolysis and combustion
- fix bond/react — template-driven reaction MD for ambient-temperature kinetics (e.g., hydrolysis, polymerization)
reaction_analysis.py— shared analysis engine: species counting, concentration profiles, first/second-order rate fitting, Arrhenius parameter extraction across multiple temperaturesbond_react_gen.py— YAML → LAMMPS native molecule template + reaction map file generator- Plot types — species timeseries (stacked area + line), reaction rate (ln[C] vs t with R²), product formation (mole fraction evolution)
Requirements:
- Linux; Schrödinger Suite (for Desmond), GROMACS, LAMMPS
- Python 3.8+ with
numpy,matplotlib,scipy - GPU recommended
| Feature | Desmond | GROMACS | LAMMPS |
|---|---|---|---|
| MD Production (EM + Equil + Prod) | ✅ | ✅ | ✅ |
| Cross-Platform Maestro (Win/Linux CRLF auto-fix) | ✅ | — | — |
| CWD Auto-Detection (no folder args) | ✅ | — | — |
| Real-Time Progress Bar | ✅ | — | — |
| Metadynamics (Well-Tempered / Standard) | ✅ (native) | ✅ (PLUMED) | ✅ (COLVARS) |
| Umbrella Sampling + WHAM | — | ✅ | — |
| Energy / T / P / Vol / Density | ✅ | ✅ | ✅ |
| H-Bond Analysis | ✅ | ✅ | — |
| RMSD / RMSF | ✅ | ✅ | ✅ |
| RDF g(r) + Coordination Number n(r) | ✅ | ✅ | ✅ |
| Radius of Gyration (Rg) | ✅ | ✅ | — |
| SASA | ✅ | ✅ | — |
| SIMA (Simulation Interactions Diagram) | ✅ | — | — |
| 1D / 2D Density Cross-Sections | ✅ | ✅ | — |
| Distance Monitoring | ✅ | — | — |
| Water Residence Time | ✅ | — | — |
| Conformational Clustering + PCA | ✅ | ✅ | ✅ |
| Molecular Dipole Moment | ✅ | — | — |
| Free Volume / Void Analysis | ✅ | — | — |
| Dihedral / Angle Analysis | — | ✅ | — |
| Contact Matrix | — | ✅ | — |
| ReaxFF Reactive MD | — | — | ✅ |
| fix bond/react Kinetics | — | — | ✅ |
| Arrhenius Rate Fitting | — | — | ✅ |
| CMS↔GROMACS/LAMMPS Converter | cms2gmx.py |
cms2lmp.py |
— |
All figures below were generated fully automatically by MOTUS from a single Desmond MD trajectory of a urea + phosphate aqueous solution. Click any engine name for the complete per-engine gallery with detailed descriptions.
| Engine | Gallery | Figures |
|---|---|---|
| Desmond | docs/images/desmond/ |
31 figures · 15 analysis types |
| GROMACS | docs/images/gromacs/ |
8 figures · 7 analysis types |
| LAMMPS | docs/images/lammps/ |
8 figures · 5 analysis types |
Before analyzing structure, verify the simulation is stable. These plots confirm the thermostat and barostat have converged — temperature, pressure, potential energy, and volume fluctuate around equilibrium values without drift.
Hydrogen bonds are the primary interaction governing solvation, molecular recognition, and interfacial structure. MOTUS tracks total and solute-specific H-bond counts, classifies water into bound / 2nd-shell / free populations, measures water residence time, and monitors solute–water contacts.
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RDF reveals the short- and medium-range order of liquids. Every element-pair g(r) is computed, with coordination number n(r) on a dual Y-axis (dashed red). Water-shell RDFs distinguish bound vs free water populations around the solute.
Density maps expose anisotropic packing, interfacial layering, or phase separation invisible in isotropic averages. 1D profiles along X/Y/Z validate homogeneity; 2D heatmaps reveal lateral structure.
Per-molecule characterization: radius of gyration (compactness), key interatomic distances (bond formation/breaking), total dipole magnitude and vector components (polarization dynamics).
Fully automated SIMA — no Maestro GUI needed. Torsion radar plots show rotatable bond dynamics via time-colored angular distributions. Ligand properties dashboard tracks RMSD, SASA, PSA, MolSA, and intramolecular H-bonds. Torsion heatmaps reveal coupled conformational preferences.
Hierarchical RMSD clustering groups trajectory frames into conformational states. The RMSD matrix heatmap visualizes pairwise structural similarity. Cluster populations (bar + pie) quantify state occupancy; the timeline shows state transitions. PCA projection onto PC1–PC2 with convex hulls and diamond centroids maps the conformational landscape. Time-colored variant reveals chronological drift.
Free volume (ų) probed by a rolling sphere + fractional free volume (FFV %). Critical for predicting gas permeability, ion conductivity, and mechanical properties in polymers, electrolytes, and porous materials.
All key metrics at a glance — temperature, energy distribution, H-bonds, and water shell populations in a 2×2 panel. Perfect for supplementary information in publications.
All figures saved in <md_output>/analysis/figures/:
| Format | Resolution | Purpose |
|---|---|---|
.pdf |
Vector | Journal submission, LaTeX inclusion |
.png |
300 DPI | Quick preview, presentations, GitHub |
Styling:
- Arial / DejaVu Sans font family
- Nature-inspired 8-color palette
- Dual Y-axis with color coding (RDF, dipole)
- Convex hulls + centroids for clustering
- Legend outside the plot frame (clean look)
- Tight bounding boxes for direct LaTeX inclusion
motus/
├── README.md ← You are here
├── LICENSE ← MIT
├── .gitignore
├── docs/images/ ← Documentation screenshots
│ ├── MOTUS-top.png ← Banner
│ ├── MOTUS-middle.png ← Overview diagram
│ ├── desmond/ ← Desmond figure gallery (+ README)
│ ├── gromacs/ ← GROMACS figure gallery (+ README)
│ └── lammps/ ← LAMMPS figure gallery (+ README)
├── desmond/ ← Desmond engine scripts
│ ├── desmond-md.sh ← MD job submission & monitoring
│ ├── desmond-analysis.sh ← Post-processing pipeline (15 modules)
│ ├── desmond-metadynamics.sh ← MetaD enhanced sampling
│ └── functions/
│ ├── desmond_plot.py ← Publication-quality figure generator
│ ├── sima_gen.py ← SIMA data generator
│ ├── sima_plot.py ← SIMA figure generator
│ ├── rdf_gen.py ← RDF + coordination number
│ ├── density_gen.py ← 1D/2D density cross-sections
│ ├── rg_gen.py ← Radius of gyration
│ ├── dist_gen.py ← Distance monitoring
│ ├── water_res_gen.py ← Water residence time
│ ├── cluster_gen.py ← Conformational clustering + PCA
│ ├── dipole_gen.py ← Molecular dipole moment
│ ├── freevol_gen.py ← Free volume / void analysis
│ ├── meta_gen.py ← Metadynamics CV setup helper
│ └── esp_gen.py ← Electrostatic potential (WIP)
│
├── gromacs/ ← GROMACS engine scripts
│ ├── gromacs-md.sh ← MD production (EM→NVT→NPT→Prod)
│ ├── gromacs-analysis.sh ← Post-processing pipeline (9 modules)
│ ├── gromacs-metadynamics.sh ← PLUMED MetaD pipeline
│ ├── gromacs-umbrella.sh ← Umbrella sampling
│ ├── gromacs-wham.sh ← WHAM PMF reconstruction
│ ├── gromacs-cluster.sh ← GROMOS conformational clustering
│ ├── gromacs-pca.sh ← PCA / essential dynamics
│ ├── gromacs-dihedral.sh ← Dihedral angle analysis
│ ├── gromacs-contacts.sh ← Distance contact maps
│ └── functions/
│ ├── gromacs_plot.py ← Figure generator (13 plot types)
│ └── gromacs_meta_gen.py ← PLUMED input generator
│
├── lammps/ ← LAMMPS engine scripts
│ ├── lammps-md.sh ← Standard MD production
│ ├── lammps-analysis.sh ← Post-processing pipeline
│ ├── lammps-metadynamics.sh ← COLVARS MetaD pipeline
│ ├── lammps-reaxff.sh ← ReaxFF reactive MD
│ ├── lammps-reaxff-analysis.sh ← ReaxFF species + kinetics analysis
│ ├── lammps-bond-react.sh ← fix bond/react template-driven MD
│ └── functions/
│ ├── lammps_plot.py ← Figure generator (9 plot types incl. reaction)
│ ├── lammps_colvars_gen.py ← COLVARS input generator
│ ├── reaction_analysis.py ← Species counting, rate fitting, Arrhenius
│ ├── bond_react_gen.py ← YAML → LAMMPS template + map generator
│ └── gen_urea_data.py ← Urea+water test system builder
│
└── converters/ ← Cross-engine CMS converters
├── cms2gmx.py ← Desmond CMS → GROMACS topology
└── cms2lmp.py ← Desmond CMS → LAMMPS data file
| Milestone | Status |
|---|---|
| Desmond post-processing (15 analyses) | ✅ |
| PCA clustering scatter with convex hulls | ✅ |
| GROMACS MD pipeline + 9 analysis scripts | ✅ |
| LAMMPS MD pipeline + 3 scripts | ✅ |
| CMS → GROMACS/LAMMPS topology converter | ✅ |
| PLUMED MetaD (GROMACS) | ✅ |
| COLVARS MetaD (LAMMPS) | ✅ |
| Umbrella sampling + WHAM (GROMACS) | ✅ |
| Cross-engine cluster plots (Desmond-style) | ✅ |
| Cross-platform Maestro (Win/Linux, CWD auto-detect, progress bar) | ✅ v0.0.3 |
| LAMMPS reactive MD — ReaxFF + fix bond/react + Arrhenius fitting | ✅ v0.0.3 |
| Solvent structure analysis (sorient/spatial/h2order) | 🚧 Planned |
| Electrostatic Potential (ESP) | 🚧 Planned |
| Unified MOTUS CLI | 🚧 Planned |
| AI-driven analysis & interpretation | 🚧 Planned |
MIT — see LICENSE file.
If you use MOTUS in your research, please cite:
MOTUS: Molecular Dynamics Automation Agent. Version 0.0.3.
https://github.com/X-Hydrogen/motus
Built for computational chemists who value their time.