Literature DB >> 29510041

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

Sereina Riniker1.   

Abstract

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Keywords:  AMBER; CHARMM; Force fields; GROMOS; Molecular dynamics simulations; OPLS

Mesh:

Year:  2018        PMID: 29510041     DOI: 10.1021/acs.jcim.8b00042

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  28 in total

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Authors:  David L Mobley; Caitlin C Bannan; Andrea Rizzi; Christopher I Bayly; John D Chodera; Victoria T Lim; Nathan M Lim; Kyle A Beauchamp; David R Slochower; Michael R Shirts; Michael K Gilson; Peter K Eastman
Journal:  J Chem Theory Comput       Date:  2018-10-30       Impact factor: 6.006

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8.  Best Practices for Foundations in Molecular Simulations [Article v1.0].

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Review 10.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
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