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      Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments

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          Abstract

          We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.

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          VMD: Visual molecular dynamics

          William Humphrey, Andrew Dalke, Klaus Schulten (1996)
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            Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

            Tom Darden, Darrin York, Nancy Pedersen (1993)
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              GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

              Berk Hess, Carsten Kutzner, David van der Spoel … (2008)
              Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.
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                Author and article information

                Contributors
                Jordi Marti: Role: Academic Editor
                Carles Calero: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Membranes (Basel)
                Journal ID (iso-abbrev): Membranes (Basel)
                Journal ID (publisher-id): membranes
                Title: Membranes
                Publisher: MDPI
                ISSN (Electronic): 2077-0375
                Publication date (Electronic): 05 July 2021
                Publication date Collection: July 2021
                Volume: 11
                Issue: 7
                Electronic Location Identifier: 507
                Affiliations
                [1 ]German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon, Lichtenbergstr. 1, 85748 Garching bei München, Germany; nebojsa.zec@ 123456hereon.de (N.Z.); gaetano.mangiapia@ 123456hereon.de (G.M.)
                [2 ]School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK; ach49@ 123456kent.ac.uk (A.C.H.); J.L.Ortega-Roldan@ 123456kent.ac.uk (J.L.O.-R.)
                [3 ]School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK; R.Barker@ 123456kent.ac.uk
                [4 ]Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, Lichtenbergstr. 1, 85748 Garching bei München, Germany; a.koutsioumpas@ 123456fz-juelich.de (A.K.); h.frielinghaus@ 123456fz-juelich.de (H.F.)
                [5 ]ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK; mario.campana@ 123456stfc.ac.uk
                Author notes
                [* ]Correspondence: sebastian.busch@ 123456hereon.de (S.B.); jean-francois.moulin@ 123456hereon.de (J.-F.M.); Tel.: +49-89-158860-764 (S.B.); +49-89-158860-762 (J.-F.M.)
                Author information
                https://orcid.org/0000-0003-4824-7988
                https://orcid.org/0000-0002-4743-3415
                https://orcid.org/0000-0002-8645-5385
                https://orcid.org/0000-0001-9417-5108
                https://orcid.org/0000-0002-8812-8783
                https://orcid.org/0000-0002-2151-4110
                https://orcid.org/0000-0002-6316-4390
                https://orcid.org/0000-0002-9815-909X
                https://orcid.org/0000-0003-2508-2607
                Article
                Publisher ID: membranes-11-00507
                DOI: 10.3390/membranes11070507
                PMC ID: 8304056
                SO-VID: 73b8063f-f914-4714-ae51-d11371a0bd00
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 02 June 2021
                Date accepted : 29 June 2021
                Categories
                Subject: Article

                Keywords: neutron reflectometry,x-ray reflectometry,small-angle neutron scattering,small-angle x-ray scattering,molecular dynamics simulations,scattering length density profile,phospholipid membrane
                Data availability:
                Keywords: neutron reflectometry, x-ray reflectometry, small-angle neutron scattering, small-angle x-ray scattering, molecular dynamics simulations, scattering length density profile, phospholipid membrane

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