Official Resources
- Homepage: https://www.htmd.org/
- Documentation: https://software.acellera.com/htmd/
- Source Repository: https://github.com/Acellera/htmd
- License: HTMD Software License
Overview
HTMD (High-Throughput Molecular Dynamics) is a programmable, extensible platform for molecular simulations. It provides tools for system preparation, simulation management, adaptive sampling, and Markov state model analysis.
Scientific domain: High-throughput MD, adaptive sampling, Markov state models
Target user community: Researchers running large-scale MD campaigns
Theoretical Methods
- Adaptive sampling
- Markov state models
- Dimensionality reduction
- Clustering algorithms
- Free energy estimation
Capabilities (CRITICAL)
- System preparation
- Simulation management
- Adaptive sampling
- Markov state model building
- Trajectory analysis
- ACEMD integration
Key Strengths
Workflow Management:
- End-to-end pipeline
- Automated preparation
- Simulation management
- Analysis tools
Adaptive Sampling:
- Intelligent sampling
- MSM-guided
- Efficient exploration
Inputs & Outputs
-
Input formats:
- PDB structures
- Various MD formats
-
Output data types:
- Prepared systems
- Trajectories
- MSM models
- Free energies
Interfaces & Ecosystem
- ACEMD: MD engine
- PyEMMA: MSM analysis
- VMD: Visualization
Advanced Features
- Adaptive sampling: MSM-guided
- System builder: Automated preparation
- MSM analysis: Kinetic modeling
- Dimensionality reduction: TICA, PCA
Performance Characteristics
- Python-based workflow
- ACEMD for MD
- Efficient analysis
- Good for campaigns
Computational Cost
- Preparation: Fast
- MD: ACEMD speed
- Analysis: Moderate
- Overall: Efficient workflow
Best Practices
- Use adaptive sampling
- Validate MSM convergence
- Check implied timescales
- Use sufficient data
Limitations & Known Constraints
- ACEMD focus
- Commercial aspects
- Learning curve
Application Areas
- Drug discovery
- Protein dynamics
- Binding kinetics
- Conformational sampling
Verification & Sources
Primary sources:
- GitHub: https://github.com/Acellera/htmd
- S. Doerr et al., J. Chem. Theory Comput. 12, 1845 (2016)
Confidence: VERIFIED
Verification status: ✅ VERIFIED
- Source code: Available (GitHub)