Demo Systems Catalog#
MolSysMT includes a built-in collection of pre-packaged molecular systems accessible via molsysmt.systems. These datasets are bundled directly with the library to enable offline testing, hands-on tutorials, benchmarks, and reproducible recipes without relying on external network downloads.
This page serves as the authoritative reference for all bundled demo systems referenced throughout the User Guide, Cookbook, Showcase, and Master Course.
How to Access Demo Systems#
All demo systems are stored in a nested dictionary structure inside molsysmt.systems, where top-level keys represent system names (such as 'Trp-Cage') and inner keys represent available file names (such as '1l2y.h5msm').
1. Listing Available Systems#
You can list all bundled system keys in Python:
import molsysmt as msm
print(list(msm.systems.keys()))
2. Accessing a System File Path#
To retrieve the absolute Path of a specific file:
file_path = msm.systems['Trp-Cage']['1l2y.h5msm']
3. Loading a System Directly into MolSysMT#
You can pass the dictionary item directly into msm.convert() or any other tool function:
molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'])
import molsysmt as msm
# Load a demo system into canonical 'molsys' variable and inspect basic attributes
molsys = msm.convert(msm.systems['Trp-Cage']['1l2y.h5msm'])
n_atoms, n_groups, n_structures = msm.get(molsys, n_atoms=True, n_groups=True, n_structures=True)
print(f"Trp-Cage loaded into molsys: {n_atoms} atoms, {n_groups} residues, {n_structures} structure(s).")
Trp-Cage loaded into molsys: 304 atoms, 20 residues, 38 structure(s).
Complete Catalog of Bundled Systems#
Below is the complete catalog of pre-packaged datasets organized by category. Each system specifies its title, dictionary keyword, architectural summary, and a detailed breakdown of all bundled file formats and their specific contents.
Dipeptides & Small Peptides
Met-Enkephalin Pentapeptide | msm.systems['Met-enkephalin']
Endogenous opioid pentapeptide (sequence Tyr-Gly-Gly-Phe-Met).
| File String | Contents & Usage Explanation |
|---|---|
'met_enkephalin.h5msm' |
Native MolSysMT HDF5 file with topology and 3D coordinates. |
'met_enkephalin.pdb' |
Protein Data Bank structure file (PDB format). |
Alanine Dipeptide | msm.systems['alanine dipeptide']
Ace-Ala-NME capped dipeptide benchmark system containing 12 heavy/hydrogen atoms.
| File String | Contents & Usage Explanation |
|---|---|
'alanine_dipeptide.h5msm' |
Native MolSysMT HDF5 file containing full topology, 12 atoms, and coordinates. |
Lysine Dipeptide | msm.systems['lysine dipeptide']
Ace-Lys-NME capped dipeptide with a positively charged sidechain.
| File String | Contents & Usage Explanation |
|---|---|
'lysine_dipeptide.h5msm' |
Native MolSysMT HDF5 file with complete topology, coordinates, and physical units. |
Pentalanine Peptide | msm.systems['pentalanine']
Uncapped Ala5 peptide benchmark dataset with Amber topology and trajectory files.
| File String | Contents & Usage Explanation |
|---|---|
'pentalanine.inpcrd' |
Amber initial coordinate file (INPCRD format). |
'pentalanine.prmtop' |
Amber molecular topology and forcefield parameter file (PRMTOP format). |
'traj_pentalanine.h5' |
HDF5 trajectory file containing coordinate frames. |
'traj_pentalanine.h5msm' |
Native MolSysMT HDF5 trajectory file containing complete dynamics and topology. |
Proline Dipeptide | msm.systems['proline dipeptide']
Ace-Pro-NME capped dipeptide featuring a cyclic pyrrolidine sidechain.
| File String | Contents & Usage Explanation |
|---|---|
'proline_dipeptide.h5msm' |
Native MolSysMT HDF5 file with complete topology, coordinates, and physical units. |
Valine Dipeptide | msm.systems['valine dipeptide']
Ace-Val-NME capped dipeptide featuring a branched aliphatic sidechain.
| File String | Contents & Usage Explanation |
|---|---|
'valine_dipeptide.h5msm' |
Native MolSysMT HDF5 file with complete topology, coordinates, and physical units. |
Small & Globular Proteins
Human Hexokinase 2 | msm.systems['Hexokinase 2']
Key glycolytic enzyme Human Hexokinase 2 bound to glucose and inhibitor (PDB 2NZT).
| File String | Contents & Usage Explanation |
|---|---|
'2nzt.bcif.gz' |
Compressed Binary CIF file (BCIF.GZ format). |
'2nzt.h5msm' |
Native MolSysMT HDF5 file containing full enzyme topology and coordinates. |
T4 Lysozyme L99A Cavity Mutant | msm.systems['T4 lysozyme L99A']
Engineered T4 lysozyme mutant with an internal hydrophobic cavity for ligand binding studies.
| File String | Contents & Usage Explanation |
|---|---|
'181l.bcif.gz' |
Compressed Binary CIF file for structure 181L. |
'181l.h5msm' |
Native MolSysMT HDF5 file for structure 181L. |
'181l.pdb' |
PDB file of the benzene-bound L99A cavity mutant (PDB 181L). |
'1l17.h5msm' |
Native MolSysMT HDF5 file for structure 1L17. |
'1l17.pdb' |
PDB file of the Apo L99A cavity mutant (PDB 1L17). |
't4_lysozyme_L99A.h5msm' |
Consolidated native MolSysMT HDF5 file for T4 lysozyme L99A. |
Trypanosoma cruzi Triosephosphate Isomerase | msm.systems['TcTIM']
Homodimeric glycolytic enzyme Triosephosphate Isomerase from Trypanosoma cruzi (PDB 1TCD).
| File String | Contents & Usage Explanation |
|---|---|
'1tcd.bcif.gz' |
Compressed Binary CIF file (BCIF.GZ format). |
'1tcd.h5msm' |
Native MolSysMT HDF5 file containing homodimer topology and 3D coordinates. |
'1tcd.pdb' |
PDB crystal structure file (PDB format). |
Trp-Cage TC5b Mini-Protein | msm.systems['Trp-Cage']
20-residue synthetic mini-protein TC5b (PDB 1L2Y) folding into a compact hydrophobic cage.
| File String | Contents & Usage Explanation |
|---|---|
'1l2y.bcif.gz' |
Compressed Binary CIF file containing full atomic coordinates and experimental metadata. |
'1l2y.h5msm' |
Native MolSysMT HDF5 file containing normalized topology, coordinates, and physical units for all 20 frames. |
'1l2y.pdb' |
PDB file containing the 20-model NMR structure ensemble. |
Chicken Villin Headpiece HP35 | msm.systems['chicken villin HP35']
35-residue fast-folding subdomain (PDB 1VII), including solvated structure and DCD trajectory.
| File String | Contents & Usage Explanation |
|---|---|
'1vii.bcif' |
Binary CIF structure file (BCIF format). |
'1vii.bcif.gz' |
Gzip-compressed Binary CIF structure file (BCIF.GZ format). |
'1vii.pdb' |
Original PDB structure file (PDB format). |
'chicken_villin_HP35.h5msm' |
Native MolSysMT HDF5 file for the vacuum protein structure. |
'chicken_villin_HP35_solvated.h5msm' |
Native MolSysMT HDF5 file for the protein solvated in a water box. |
'traj_chicken_villin_HP35_solvated.dcd' |
CHARMM/NAMD DCD binary trajectory file of solvated dynamics. |
'traj_chicken_villin_HP35_solvated.h5' |
HDF5 trajectory file containing coordinate frames. |
'traj_chicken_villin_HP35_solvated.h5msm' |
Native MolSysMT HDF5 trajectory file with solvated protein dynamics. |
Complexes & Assemblies
PKA Kinase Complex | msm.systems['1ATP']
cAMP-dependent protein kinase catalytic subunit complexed with Mn2+ ATP and inhibitor (PDB 1ATP).
| File String | Contents & Usage Explanation |
|---|---|
'1atp.bcif.gz' |
Compressed Binary CIF file for 1ATP complex. |
'1atp.pdb' |
PDB structure file with HETSYN hetero-group records. |
CENP-B DNA-Binding Domain | msm.systems['1CEN']
Centromere protein B DNA-binding domain crystal structure (PDB 1CEN).
| File String | Contents & Usage Explanation |
|---|---|
'1cen.bcif.gz' |
Compressed Binary CIF file for 1CEN structure. |
'1cen.pdb' |
PDB structure file with HETSYN hetero-group records. |
MDM2 - p53 Peptide Complex | msm.systems['1YCR']
Human MDM2 oncogene bound to the p53 transactivation domain peptide (PDB 1YCR).
| File String | Contents & Usage Explanation |
|---|---|
'1ycr.bcif.gz' |
Compressed Binary CIF file for 1YCR complex. |
'1ycr.pdb' |
PDB structure file featuring SOURCE records without trailing semicolons. |
Ribosome Structural Benchmark | msm.systems['2HGR']
Split/obsolete ribosome structural benchmark dataset (PDB 2HGR).
| File String | Contents & Usage Explanation |
|---|---|
'2hgr.pdb' |
Original PDB structure file with OBSLTE and SPLIT records. |
Thermus thermophilus 70S Ribosome | msm.systems['4V4Z']
Macromolecular 70S ribosome assembly (PDB 4V4Z) containing 149,640 atoms.
| File String | Contents & Usage Explanation |
|---|---|
'4v4z.bcif.gz' |
Compressed Binary CIF file supporting atom counts exceeding standard PDB limits. |
'4v4z_openmm.pdb' |
OpenMM PDB file with uppercase hex serial overflow formatting. |
Barnase-Barstar Protein-Protein Complex | msm.systems['Barnase-Barstar']
Ultra-high affinity complex between bacterial ribonuclease Barnase and inhibitor Barstar (PDB 1BRS).
| File String | Contents & Usage Explanation |
|---|---|
'1brs.bcif' |
Binary CIF structure file for the 1BRS complex. |
'1brs.bcif.gz' |
Compressed Binary CIF structure file. |
'1brs.h5msm' |
Native MolSysMT HDF5 file for 1BRS crystal structure. |
'barnase_barstar.h5msm' |
Consolidated native MolSysMT HDF5 file for the Barnase-Barstar complex. |
Small Molecules & Ligands
Benzamidine Ligand | msm.systems['benzamidine']
Benzamidine synthetic aromatic inhibitor ligand.
| File String | Contents & Usage Explanation |
|---|---|
'benzamidine.pdb' |
PDB format structure file for benzamidine. |
Caffeine Small Molecule | msm.systems['caffeine']
Caffeine xanthine alkaloid small molecule.
| File String | Contents & Usage Explanation |
|---|---|
'caffeine.mol2' |
Tripos MOL2 format file containing bond types, atom types, and partial charges. |
Lipids & Membranes
POPC Lipid Molecule | msm.systems['POPC']
Single POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) zwitterionic lipid molecule.
| File String | Contents & Usage Explanation |
|---|---|
'popc.crd' |
CHARMM CRD coordinate file. |
'popc.psf' |
CHARMM PSF protein/lipid structure file. |
POPC Lipid Bilayer Membrane | msm.systems['POPC membrane']
Hydrated POPC lipid bilayer membrane simulation system and trajectory.
| File String | Contents & Usage Explanation |
|---|---|
'popc_membrane.dcd' |
CHARMM/NAMD DCD binary trajectory file of membrane dynamics. |
'popc_membrane.psf' |
CHARMM PSF topology file for the lipid bilayer system. |
Toy & Synthetic Models
NGLView Bridge Test Suite | msm.systems['nglview']
Specialized test files for NGLView, MDTraj, and GROMACS interoperability bridges.
| File String | Contents & Usage Explanation |
|---|---|
'ala3.pdb' |
Tri-alanine peptide PDB structure file. |
'md_1u19.gro' |
GROMACS GRO structure file for PDB 1U19. |
'md_1u19.pdb' |
PDB structure file for PDB 1U19. |
'md_1u19.traj' |
MDTraj trajectory file. |
'md_1u19.trr' |
GROMACS TRR full-precision binary trajectory file. |
'md_1u19.xtc' |
GROMACS XTC compressed binary trajectory file. |
Particles 4 Trajectory | msm.systems['particles 4']
4-particle spatial coordinate trajectory.
| File String | Contents & Usage Explanation |
|---|---|
'traj_particles_4.xyznpy' |
NumPy NPY binary array file containing (n_frames, 4, 3) coordinates. |
Two Lennard-Jones Particles | msm.systems['two LJ particles']
Minimalist 2-particle Lennard-Jones toy system trajectory.
| File String | Contents & Usage Explanation |
|---|---|
'traj_two_lj_particles.trjpk' |
Pickled trajectory file for algorithmic unit testing. |
Offline Accessibility
All datasets in molsysmt.systems are pre-packaged with the library. You can run all tutorials and test suites completely offline without requiring internet access.