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- Title
Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations.
- Authors
Schreiner, Wolfgang; Karch, Rudolf; Knapp, Bernhard; Ilieva, Nevena
- Abstract
Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals ?t. Unless RMSD(?t) has reached a stationary shape, the simulation has not yet converged.
- Subjects
RELAXATION for health; MOLECULAR dynamics; MATHEMATICAL proofs; STOCHASTIC convergence; STANDARD deviations; MOLECULAR shapes
- Publication
Computational & Mathematical Methods in Medicine, 2012, p1
- ISSN
1748-670X
- Publication type
Article
- DOI
10.1155/2012/173521