HpTonB(30-285) Molecular Dynamics Simulation Trajectories with Amber ff03ws

Molecular dynamics simulation data of the periplasmic part of the TonB protein from Helicobacter pylori. The dataset contains trajectory files from a simulation using the Amber ff03ws force field with 40 mM NaCl, including the last 1000 nanoseconds of the run. It was produced by I. Salla Virtanen at the University of Helsinki.

Use Cases

• Analyzing protein conformational dynamics based on the 1000ns simulation trajectory.
• Validating the Amber ff03ws force field for protein-solvent systems based on the described simulation parameters.
• Studying ion-protein interactions based on the 40 mM NaCl solvent environment mentioned in the description.
• Comparing simulation trajectories with different saving frequencies (10 ps vs 100 ps) for analysis efficiency.

Strengths

• Simulation covers a long 1000 nanosecond trajectory, which is useful for observing slower protein dynamics.
• Provides both protein-only and protein-solvent system files, allowing for focused or holistic analysis.
• Uses a specific, documented force field (Amber ff03ws) with publicly available parameter sources.

Limitations

• Row count and dataset size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Helsinki, I. Salla Virtanen

Collection Method

Molecular dynamics simulation performed with GROMACS (inferred from .tpr and .gro file formats).