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The effects of truncating long-range forces on protein dynamics
1Molecular Graphics and Simulation Laboratory, National Institutes of Health, Bethesda, Maryland 20892.
Proteins
|January 1, 1989
Summary
Truncating long-range forces in protein dynamics simulations significantly impacts results. A shifted potential method shows reasonable protein behavior at cutoff distances of 14 Å or larger.
Area of Science:
- Computational Biology
- Molecular Dynamics
- Protein Dynamics
Background:
- Accurate simulation of protein dynamics requires modeling long-range forces.
- Truncating these forces is computationally necessary but can introduce artifacts.
Purpose of the Study:
- To evaluate the impact of various long-range force truncation methods on protein dynamics simulations.
- To determine optimal truncation strategies for reliable protein behavior modeling.
Main Methods:
- Investigated six truncation methods: shifted potential, switching function, and distance/list-based atom-atom and group-group truncation.
- Performed 70 carboxymyoglobin simulations with varying cutoff criteria.
- Evaluated simulations based on root-mean-square (RMS) fluctuation and deviation from no-cutoff and X-ray structures.
Main Results:
- Shifted potential method yielded reasonable results at cutoff distances ≥ 14 Å.
- Distance-based atom-atom and group-group truncation showed good results for cutoffs ≥ 11 Å.
- List-based truncation methods were less stable than distance-based ones.
Conclusions:
- The choice of truncation method and cutoff distance critically affects protein dynamics simulations.
- Shifted potential and distance-based truncation methods offer viable strategies for simulating protein behavior.