Calculating potentials of mean force from steered molecular dynamics simulations.

By Sanghyun Park, Klaus Schulten. Journal of Chemical Physics, 2004

815 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Physical and Theoretical Chemistry, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/e7e8d28f20791f9db4fb7ff97ccefb7249c7a5d4

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Citations in the corpus

Scalable molecular dynamics with NAMD (2005, methodology): “The relationship between the Langevin equation and the associated Fokker-Planck equation has been invoked, for example, in [41].”
Biological and synthetic membranes: What can be learned from a coarse-grained description? (2006, methodology): “If this is repeated often enough, Jarzynski’s equation [101–105] can be used to calculate free energies by integrating the corresponding Boltzmann factor.”
QM/MM Methods for Biological Systems (2006, background): “This relation has become the foundation for “fast-growth” [351] or “multiple-steering” [349, 352, 353] simulations, in which irreversible-work values from deliberately non-adiabatic switching processes are accumulated and exponentially averaged according to Eq.”
Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants (2007, methodology): “A series of steered MD (SMD) [ 27 ] is used to estimate the work based on Jarzynski's equality [ 28 ].”
Nonequilibrium fluctuations in small systems: From physics to biology (2007, methodology): “Free-energy recovery techniques are also used in numerical simulations to evaluate free-energy differences [105, 106, 107, 108] and reconstruct free-energy profiles or potentials of mean-field force [109, 110].”
Stochastic predictions of interfacial characteristic of polymeric nanocomposites (PNCs) (2014, neutral): “More details can be found in [32].”
Stochastic thermodynamics, fluctuation theorems and molecular machines (2012, background): “Some of the papers dealing with this issue are [86, 137, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480].”
Discovery Through the Computational Microscope (2009, neutral): “…dynamics (SMD) simulations (Izrailev et al., 1999; Isralewitz et al., 2001b, 2001a; Grubmüller, 2005), bridging the timescale gap between experiment and simulation through a theoretical framework (Izrailev et al., 1997; Evans and Ritchie, 1997; Park and Schulten, 2004; Evans and Calderwood, 2007).”