Recovering position-dependent diffusion from biased molecular dynamics simulations

Journal Article · Fri Feb 28 04:00:00 EST 2014 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4866448· OSTI ID:22255050

Ljubetič, Ajasja; Urbančič, Iztok; Štrancar, Janez ^[1]

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1. Laboratory of Biophysics, Condensed Matter Physics Department, “Jožef Stefan” Institute, 1000 Ljubljana (Slovenia)

All atom molecular dynamics (MD) models provide valuable insight into the dynamics of biophysical systems, but are limited in size or length by the high computational demands. The latter can be reduced by simulating long term diffusive dynamics (also known as Langevin dynamics or Brownian motion) of the most interesting and important user-defined parts of the studied system, termed collective variables (colvars). A few hundred nanosecond-long biased MD trajectory can therefore be extended to millisecond lengths in the colvars subspace at a very small additional computational cost. In this work, we develop a method for determining multidimensional anisotropic position- and timescale-dependent diffusion coefficients (D) by analysing the changes of colvars in an existing MD trajectory. As a test case, we obtained D for dihedral angles of the alanine dipeptide. An open source Mathematica{sup ®} package, capable of determining and visualizing D in one or two dimensions, is available at https://github.com/lbf-ijs/DiffusiveDynamics . Given known free energy and D, the package can also generate diffusive trajectories.

• OSTI ID: 22255050
• Journal Information: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 8 Vol. 140; ISSN JCPSA6; ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
ALANINES
ANISOTROPY
BROWNIAN MOVEMENT
DIFFUSION
FREE ENERGY
MOLECULAR DYNAMICS METHOD
SIMULATION