23
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

      Preprint
      ,

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.

          Related collections

          Most cited references149

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Escaping free-energy minima

          We introduce a novel and powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of a coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates.A characteristic feature of this dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the free energy surface, allowing the efficient exploration and accurate determination of the free energy surface as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Constrained reaction coordinate dynamics for the simulation of rare events

              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              Free energy calculations: Applications to chemical and biochemical phenomena

                Bookmark

                Author and article information

                Journal
                02 January 2014
                Article
                10.3390/e16010163
                1401.0387
                b15130dd-b247-45ec-b611-aca07ed13c5f

                http://creativecommons.org/licenses/by/3.0/

                History
                Custom metadata
                C. Abrams and G. Bussi, Entropy 16, 163 (2014)
                Accepted for publication on Entropy
                cond-mat.stat-mech physics.chem-ph physics.comp-ph

                Comments

                Comment on this article