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SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions

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Molecular Dynamics Group, Groningen Institute for Biotechnology and Biomolecular Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
§ Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, POB 800, 9700 AV, Groningen, The Netherlands
*Phone: +31.(0)50-3634336. Fax: +31.(0)50-3634800. E-mail: [email protected]
Cite this: J. Chem. Theory Comput. 2012, 8, 10, 3618–3627
Publication Date (Web):May 28, 2012
https://doi.org/10.1021/ct3000662
Copyright © 2012 American Chemical Society

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    Abstract

    In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent–solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php.

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    Cited By

    This article is cited by 4 publications.

    1. R. Gregor Weiß, Marie-Estelle Losfeld, Markus Aebi, Sereina Riniker. N-Glycosylation Enhances Conformational Flexibility of Protein Disulfide Isomerase Revealed by Microsecond Molecular Dynamics and Markov State Modeling. The Journal of Physical Chemistry B 2021, 125 (33) , 9467-9479. https://doi.org/10.1021/acs.jpcb.1c04279
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    3. Corina Mathew, R. Gregor Weiß, Christoph Giese, Chia-wei Lin, Marie-Estelle Losfeld, Rudi Glockshuber, Sereina Riniker, Markus Aebi. Glycan–protein interactions determine kinetics of N -glycan remodeling. RSC Chemical Biology 2021, 2 (3) , 917-931. https://doi.org/10.1039/D1CB00019E
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