A Fast and Parallelized Procedure for Checking Molecular Dynamics 3D Structure
Daniel R Roe, Bernard R Brooks · 2026
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Description
Daniel Roe and Bernard Brooks detailed in 2026 a fast check for broken molecular structures. Models built for molecular dynamics simulations often carry flaws: wrong handedness, clashing atoms, stretched bonds, or rings passing through each other. Such defects can crash a simulation before it starts. Their procedure hunts the common problems in an automated way.
The check targets atomic overlaps, distorted bonds, and ring intersections among other issues. It is parallelized so that structures with millions of atoms can be scanned quickly. Speed matters because modern simulations start from huge assembled systems. Catching a flaw early saves wasted compute and confusing failures. The authors present the method as routine hygiene for simulation work. Structural biology and drug design pipelines are natural users.
Catalog record
| CREATOR | Daniel R Roe, Bernard R Brooks |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 38 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |