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Relaxation estimation of RMSD in molecular dynamics immunosimulations.

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 Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

SUBMITTER: Schreiner W

PROVIDER: S-EPMC3457668 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Relaxation estimation of RMSD in molecular dynamics immunosimulations.

Schreiner Wolfgang W Karch Rudolf R Knapp Bernhard B Ilieva Nevena N

Computational and mathematical methods in medicine 20120916

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 Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged. ...[more]

PMID: 23019425

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Dataset Information

Relaxation estimation of RMSD in molecular dynamics immunosimulations.

Publications

Relaxation estimation of RMSD in molecular dynamics immunosimulations.

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