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Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules
- Source :
- Molecular Simulation. 29:471-478
- Publication Year :
- 2003
- Publisher :
- Informa UK Limited, 2003.
-
Abstract
- We report a multiple time step algorithm applied to an atomistic Brownian dynamics simulation for simulating the long time scale dynamics of biomolecules. The algorithm was based on the original multiple time step method; a short time step was used to keep faster motions in local equilibrium. When applied to a 28-mer # # ! folded peptide, the simulation gave stable trajectories and the computation time was reduced by a factor of 160 compared to a conventional molecular dynamics simulation using explicit water molecules. We applied it for the folding simulation of a 13-mer ! -helical peptide, giving a successful folding simulation. These results indicate that the Brownian dynamics with the multiple time step algorithm is useful for studies of biomolecular motions by long time simulation.
- Subjects :
- Physics
chemistry.chemical_classification
Quantitative Biology::Biomolecules
Scale (ratio)
General Chemical Engineering
Computation
Biomolecule
Dynamics (mechanics)
General Chemistry
Folding (DSP implementation)
Condensed Matter Physics
Molecular dynamics
chemistry
Modeling and Simulation
Brownian dynamics
Multiple time
General Materials Science
Statistical physics
Information Systems
Subjects
Details
- ISSN :
- 10290435 and 08927022
- Volume :
- 29
- Database :
- OpenAIRE
- Journal :
- Molecular Simulation
- Accession number :
- edsair.doi...........23a6af7854a783e3ee62bcb0f5e4cec2