SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and
José García de la Torre1, José G Hernández Cifre1, Álvaro Ortega1
1Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway.
Abstract:
A computer programs suite, SIMUFLEX, has been constructed for the calculation of solution properties of flexible macromolecules modeled as bead-and-connector models of arbitrary topology. The suite consists mainly of two independent programs, BROWFLEX that generates the macromolecular trajectory by using the Brownian dynamics technique and ANAFLEX that analyzes that trajectory to get solution properties of the macromolecule. In this paper, we describe theoretical aspects about the macromolecular model and the Brownian dynamics algorithm used and describe some of the numerous properties that can be evaluated. In order to provide examples of the application of the methodology, we present simulations of dynamic properties of DNA with length ranging from 10 to 10(5) base pairs. SIMUFLEX is able to run simulations with more or less coarse-grained models, thus enabling such multiple-scale studies.
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