Local elevation

Local elevation is a technique used in computational chemistry or physics, mainly in the field of molecular simulation (including molecular dynamics (MD) and Monte Carlo (MC) simulations). It was developed in 1994 by Huber, Torda and van Gunsteren [1] to enhance the searching of conformational space in molecular dynamics simulations and is available in the GROMOS software for molecular dynamics simulation (since GROMOS96). The method was, together with the conformational flooding method, [2] the first to introduce memory dependence into molecular simulations. Many recent methods build on the principles of the local elevation technique, including the Engkvist-Karlström, [3] adaptive biasing force, [4] Wang–Landau, metadynamics, adaptively biased molecular dynamics, [5] adaptive reaction coordinate forces, [6] and local elevation umbrella sampling [7] methods. The basic principle of the method is to add a memory-dependent potential energy term in the simulation so as to prevent the simulation to revisit already sampled configurations, which leads to the increased probability of discovering new configurations. The method can be seen as a continuous variant of the Tabu search method.

  1. ^ Huber, T.; Torda, A.E.; van Gunsteren, W.F. (1994). "Local elevation: A method for improving the searching properties of molecular dynamics simulation". J.Comput.-Aided Mol. Design. 8 (6): 695–708. Bibcode:1994JCAMD...8..695H. doi:10.1007/BF00124016. PMID 7738605. S2CID 15839136.
  2. ^ Grubmüller, H. (1995). "Predicting slow structural transitions in macromolecular systems: conformational flooding" (PDF). Phys. Rev. E. 52 (3): 2893–2906. Bibcode:1995PhRvE..52.2893G. doi:10.1103/PhysRevE.52.2893. hdl:11858/00-001M-0000-000E-CA15-8. PMID 9963736.
  3. ^ Engkvist, O.; Karlström, G. (1996). "A method to calculate the probability distribution for systems with large energy barriers". Chem. Phys. 213 (1–3): 63–76. Bibcode:1996CP....213...63E. doi:10.1016/S0301-0104(96)00247-9.
  4. ^ Darve, E.; Pohorille, A. (2001). "Calculating free energies using average force". J. Chem. Phys. 115 (20): 9169–9183. Bibcode:2001JChPh.115.9169D. doi:10.1063/1.1410978. hdl:2060/20010090348. S2CID 5310339.
  5. ^ Babin, V.; Roland, C.; Sagui, C. (2008). "Stabilization of resonance states by an asymptotic Coulomb potential". J. Chem. Phys. 128 (2): 134101/1–134101/7. Bibcode:2008JChPh.128b4101A. doi:10.1063/1.2821102. PMID 18205437.
  6. ^ Barnett, C.B.; Naidoo, K.J. (2009). "Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): An application to ring puckering". Mol. Phys. 107 (8–12): 1243–1250. Bibcode:2009MolPh.107.1243B. doi:10.1080/00268970902852608. S2CID 97930008.
  7. ^ Hansen, H.S.; Hünenberger, P.H. (2010). "Using the Local Elevation Method to Construct Optimized Umbrella Sampling Potentials: Calculation of the Relative Free Energies and Interconversion Barriers of Glucopyranose Ring Conformers in Water". J. Comput. Chem. 31 (1): 1–23. doi:10.1002/jcc.21253. PMID 19412904. S2CID 7367058.