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Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0002-4591-9809
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0003-0603-5514
KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0001-6363-2521
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2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 12, 5737-5746 p.Article in journal (Refereed) PublishedText
Abstract [en]

Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2015. Vol. 11, no 12, 5737-5746 p.
National Category
Physical Sciences
URN: urn:nbn:se:kth:diva-180232DOI: 10.1021/acs.jctc.5b00726ISI: 000366223400017PubMedID: 26587968ScopusID: 2-s2.0-84949640540OAI: diva2:895418

QC 20160119

Available from: 2016-01-19 Created: 2016-01-08 Last updated: 2016-05-20Bibliographically approved
In thesis
1. Computational modeling of biological barriers
Open this publication in new window or tab >>Computational modeling of biological barriers
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

One of the most important aspects for all life on this planet is the act to keep their biological processes in a state where they do not reach equilibrium. One part in the upholding of this imbalanced state is the barrier between the cells and their surroundings, created by the cell membrane. Additionally, terrestrial animal life often requires a barrier that protects the organism's body from external hazards and water loss. As an alternative to experiments, the investigation of the processes occurring at these barriers can be performed by using molecular dynamics simulations. Through this method we can obtain an atomistic description of the dynamics associated with events that are not accessible to experimental setups.

 In this thesis the first paper presents an improved particle-mesh Ewald method for the calculation of long-range Lennard-Jones interactions in molecular dynamics simulations, which solves the historical performance problem of the method. The second paper demonstrate an improved implementation, with a higher accuracy, that only incurs a performance loss of roughly 15% compared to conventional simulations using the Gromacs simulation package. Furthermore, the third paper presents a study of cholesterol's effect on the permeation of six different solutes across a variety of lipid bilayers. A laterally inhomogeneous permeability in cholesterol-containing membranes is proposed as an explanation for the large differences between experimental permeabilities and calculated partition coefficients in simulations. The fourth paper contains a coarse-grained simulation study of a proposed structural transformation in ceramide bilayer structures, during the formation of the stratum corneum. The simulations show that glycosylceramides are able to stabilize a three-dimensionally folded bilayer structure, while simulations with ceramides collapse into a lamellar bilayer structure.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2016. xii, 49 p.
TRITA-FYS, ISSN 0280-316X ; 2016:10
Molecular dynamics, cholesterol, lipid bilayer, permeability, long-range interactions, Lennard-Jones, dispersion, particle-mesh Ewald, stratum corneum, skin formation
National Category
Research subject
Biological Physics
urn:nbn:se:kth:diva-183362 (URN)978-91-7595-884-2 (ISBN)
Public defence
2016-04-15, sal F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (English)

QC 20160308

Available from: 2016-03-08 Created: 2016-03-08 Last updated: 2016-03-09Bibliographically approved

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Wennberg, Christian L.Murtola, TeemuPall, SzilardAbraham, Mark JamesHess, BerkLindahl, Erik
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