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- W3132828321 abstract "Abstract A methodology is proposed for calculating multidimensional free-energy landscapes of molecular systems, based on post-hoc analysis of multiple molecular dynamics trajectories wherein adaptive biases are used to enhance the sampling of different collective variables. In this approach, which we refer to as Force Correction Analysis Method (FCAM), total and biasing forces from all trajectories are subtracted and combined in the form of local averages, so as to obtain unbiased estimates of the mean forces across collective-variable space; multidimensional free-energy surfaces and minimum-energy pathways are then derived from integration of the mean forces through kinetic Monte Carlo simulations. Numerical tests for trajectories of butyramide generated with standard and concurrent metadynamics, biased to sample one and two dihedral angles, respectively, as well as metadynamics simulations of deca-L-alanine reversible unfolding, demonstrate the correctness of the method and show that calculated mean forces and free energies converge rapidly. Analysis of bias-exchange metadynamics simulations of dialanine, trialanine and the SH2-SH3 domain-tandem of the Abl kinase, using up to six collective-variables, further demonstrate this approach greatly facilitates calculating accurate multidimensional free-energy landscapes from different trajectories and time-dependent biases, outperforming other post-hoc unbiasing methods." @default.
- W3132828321 created "2021-03-01" @default.
- W3132828321 creator A5066819680 @default.
- W3132828321 creator A5082200811 @default.
- W3132828321 date "2021-02-18" @default.
- W3132828321 modified "2023-10-18" @default.
- W3132828321 title "Force correction analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations" @default.
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- W3132828321 doi "https://doi.org/10.1101/2021.02.17.431654" @default.
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