Molecular Dynamics

Molecular Dynamics Trajectory Analysis

Overview

This skill turns raw MD trajectories into quantitative conformational descriptors. It ships a self-contained pure-numpy DCD parser (DCD is a Fortran-style fixed-length record stream: an 84-byte header record followed by per-frame coordinate records), so a trajectory produced by NAMD, CHARMM, GROMACS or LAMMPS can be analysed without installing MDAnalysis. A multi-model PDB parser and an XYZ parser are provided as well, and MDAnalysis is used automatically when it is available.

All core algorithms are implemented directly and are numerically well-defined:

• Kabsch-Sander optimal rigid-body superposition via SVD of the covariance matrix (with the determinant correction that prevents reflection).
• PCA by eigendecomposition of the coordinate covariance matrix.
• Hierarchical clustering (average/complete/ward linkage) of the pairwise RMSD matrix.
• Hydrogen bonds by a distance + angle geometric criterion.
• Shrake-Rupley solvent-accessible surface area.
• Ramachandran region assignment from backbone φ/ψ dihedrals.

run_simulation.py drives a real MD run through OpenMM when OpenMM is installed (force-field setup, Langevin thermostat, minimisation, equilibration, production run, DCD output).

When to Use This Skill

• RMSD / RMSF / radius-of-gyration time series from a DCD trajectory
• Principal component analysis of conformational motion
• Clustering a trajectory into conformational states (RMSD matrix + linkage)
• Hydrogen-bond counts and occupancy across frames
• Ramachandran distribution and secondary-structure validation of a trajectory
• Inter-chain contact stability in a protein–protein or protein–ligand complex
• Solvent-accessible surface area and buried-surface estimation
• Reading DCD files without installing MDAnalysis
• Running a short MD simulation with OpenMM

Quick Start

bashCopy code
# 基础分析（DCD + 拓扑 PDB）
python scripts/run_analysis.py --input traj.dcd --topology system.pdb \
    --output results/

# 只算 RMSD 与 RMSF
python scripts/run_analysis.py --input traj.dcd --topology system.pdb \
    --analysis rmsd,rmsf --output results/

# 跳过平衡阶段（只看生产段）
python scripts/run_analysis.py --input traj.dcd --topology system.pdb \
    --start 500 --stride 2 --output results/

# 按簇数做构象聚类
python scripts/run_analysis.py --input traj.dcd --topology system.pdb \
    --analysis cluster --n-clusters 5 --output results/

# 用 OpenMM 跑一段模拟（生产期）
python scripts/run_simulation.py --input system.pdb --output results/ --steps 100000

# 复合物的分阶段平衡协议（NVT → NPT → 生产期，带位置限制）
python scripts/run_simulation.py --input complex.pdb --output results/ \
    --nvt-steps 50000 --npt-steps 50000 --restraints backbone \
    --monitor-chain-separation --steps 500000

# 生产期也保持弱位置限制（k=10 kJ/mol/Ų）
python scripts/run_simulation.py --input complex.pdb --output results/ \
    --nvt-steps 50000 --restraints backbone --production-restraint-force-constant 10

Workflow

Analysis path

1. Load — trajectory_io.py reads the trajectory. MDAnalysis is tried first; otherwise the built-in parsers handle .dcd (Fortran record stream), .pdb (multi-model) and .xyz. Topology (atom names, elements, chains, residues) comes from the --topology PDB when supplied.
2. Select — the selection string (protein, name CA, resname LIG, resid 1-50, chain A) is resolved to an atom index array; masses are attached for mass-weighted quantities.
3. Superpose — every frame is aligned to the reference frame by kabsch_align, giving the rotation matrix, translation and residual RMSD.
4. Analyse — RMSD (global + per-residue Cα), RMSF, radius of gyration, hydrogen bonds, PCA, dihedral series, Ramachandran, conformational clustering, inter-chain contacts and SASA.
5. Report — writes md_analysis.json and md_analysis_frames.csv.

Simulation path (run_simulation.py)

The simulation follows a staged equilibration protocol, which is the standard way to avoid the two classic failure modes of complex simulations: chains drifting apart during equilibration, and sampling a structure that never relaxed out of its crystal-packing geometry.

1. Minimise — simulation.minimizeEnergy() removes the steric clashes inherited from the input structure.
2. NVT equilibration (--nvt-steps) — constant volume, velocities re-drawn at the target temperature. Optional position restraints (--restraints) hold the backbone in place so only side chains and solvent relax.
3. NPT equilibration (--npt-steps) — a MonteCarloBarostat is added and the simulation is rebuilt so the pressure coupling takes effect on the density.
4. Production — position restraints are removed by default (use --production-restraint-force-constant to keep a weak version). Chain separation is monitored throughout if --monitor-chain-separation is set.
5. Stability check — the final coordinates are screened for NaN / Inf / numerical blow-up; if found, the simulation is rolled back to the input structure and the reason is recorded in the report.

Implementation note. Position restraints must be added to the System before the Simulation (and therefore the Context) is created — modifying system afterwards does not rebuild the context, so the force would silently never take effect. The same applies when adding the barostat or removing the restraints: the simulation is rebuilt and positions plus velocities are carried over.

Parameters

run_simulation.py 额外参数：

Outputs

Validation

• RMSD must start near zero: the frame used as --fit-reference must have RMSD ≈ 0 by construction. If not, the alignment code path is broken.
• RMSD is bounded by the drift: a trajectory with a global translation of 0.02 Å/frame must show a roughly linear RMSD growth after superposition; a flat curve means the superposition is absorbing the motion.
• RMSF sanity: for a well-folded globular domain, mean Cα RMSF is typically 0.5-2 Å; values above 5 Å indicate an unstable or badly parameterised simulation. Values below 0.01 Å mean the trajectory is frozen or the frames are identical.
• Rg vs structure: Rg ≈ 2.2 × N^0.38 Å is a common empirical rule for globular proteins. A sudden jump in Rg usually indicates unfolding.
• Hydrogen bonds: a stable protein in water shows 50-200 backbone-sidechain and backbone-backbone hydrogen bonds per frame. Zero hydrogen bonds with non-zero donors and acceptors means the topology lacks hydrogen atoms (X-ray structures) — add them before analysis.
• PCA: the first principal component of a globular protein usually explains 30-60% of the variance. A single component explaining >95% usually means global translation/rotation was not removed before the analysis.
• Clustering: the number of clusters must be consistent with the RMSD matrix structure. If all frames land in one cluster while the RMSD range is wide, the linkage threshold is too large.
• Ramachandran: a well-behaved simulation has fewer than 0.5% outliers in the allowed regions. More outliers indicates either force-field problems or an incorrect topology (e.g. broken backbone connectivity).
• SASA: for a 100-residue globular protein, total SASA is typically 5000-7000 Ų. Much lower values indicate collapsed/over-packed structures.
• DCD parsing: the parsed n_atoms must match the topology atom count; a mismatch means the DCD and topology do not correspond.
• Equilibration stages: simulation_report.json → stages must list every stage that was requested. A requested --nvt-steps that does not appear means the stage was silently skipped.
• Chain separation: when --monitor-chain-separation is on, the chain_separation block must exist and final_check.separated must be false for a stable complex. A true value means the chains drifted apart — check the starting structure (usually a docking pose that was never relaxed) before trusting any downstream analysis.
• Restraint effect: with --restraints backbone on, the NVT trajectory must show a noticeably smaller backbone RMSD than an unrestrained run. If the numbers are identical, the restraints never took effect — this happens when the force is added to the System after the Context was created.
• Stability: stability.should_rollback must be false for a healthy run. If it is true, the report's stability.reason explains whether the coordinates went NaN, hit Inf, or blew up numerically — a NaN in the very first frames usually points at a bad force field or missing hydrogens rather than at the dynamics themselves.

References

• references/methodology.md — algorithms, formulas and parameter rationale
• references/troubleshooting.md — common failures and how to diagnose them