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Publications (10 of 48) Show all publications
Shamshirgar, D. S., Yokota, R., Tornberg, A.-K. & Hess, B. (2019). Regularizing the fast multipole method for use in molecular simulation. Journal of Chemical Physics, 151(23), Article ID 234113.
Open this publication in new window or tab >>Regularizing the fast multipole method for use in molecular simulation
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 23, article id 234113Article in journal (Refereed) Published
Abstract [en]

The parallel scaling of classical molecular dynamics simulations is limited by the communication of the 3D fast Fourier transform of the particle-mesh electrostatics methods, which are used by most molecular simulation packages. The Fast Multipole Method (FMM) has much lower communication requirements and would, therefore, be a promising alternative to mesh based approaches. However, the abrupt switch from direct particle-particle interactions to approximate multipole interactions causes a violation of energy conservation, which is required in molecular dynamics. To counteract this effect, higher accuracy must be requested from the FMM, leading to a substantially increased computational cost. Here, we present a regularization of the FMM that provides analytical energy conservation. This allows the use of a precision comparable to that used with particle-mesh methods, which significantly increases the efficiency. With an application to a 2D system of dipolar molecules representative of water, we show that the regularization not only provides energy conservation but also significantly improves the accuracy. The latter is possible due to the local charge neutrality in molecular systems. Additionally, we show that the regularization reduces the multipole coefficients for a 3D water model even more than in our 2D example.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2019
National Category
Mathematics
Identifiers
urn:nbn:se:kth:diva-269502 (URN)10.1063/1.5122859 (DOI)000513157600016 ()31864270 (PubMedID)2-s2.0-850770017852-s2.0-85077001785 (Scopus ID)
Note

QC 20200309

Available from: 2020-03-09 Created: 2020-03-09 Last updated: 2020-03-09Bibliographically approved
Elofsson, A., Hess, B., Lindahl, E., Onufriev, A., van der Spoel, D. & Wallqvist, A. (2019). Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PloS Computational Biology, 15(1), Article ID e1006649.
Open this publication in new window or tab >>Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
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2019 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 15, no 1, article id e1006649Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2019
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:kth:diva-244559 (URN)10.1371/journal.pcbi.1006649 (DOI)000457372500019 ()30653494 (PubMedID)2-s2.0-85060153842 (Scopus ID)
Note

QC 20190312

Available from: 2019-03-12 Created: 2019-03-12 Last updated: 2020-03-05Bibliographically approved
Johansson, P. & Hess, B. (2018). Molecular origin of contact line friction in dynamic wetting. Physical Review Fluids, 3(7), Article ID 074201.
Open this publication in new window or tab >>Molecular origin of contact line friction in dynamic wetting
2018 (English)In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, no 7, article id 074201Article in journal (Refereed) Published
Abstract [en]

A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact line can advance during wetting. Using large-scale molecular dynamics simulations we show that the contact line advances by single molecules moving ahead of the contact line through two distinct processes: either moving over or displacing other liquid molecules. In both processes friction occurs at the molecular scale. We measure the energy dissipation at the contact line and show that it is of the same magnitude as the dissipation in the bulk of a droplet. The friction increases significantly as the contact angle decreases, which suggests suggests thermal activation plays a role. We provide a simple model that is consistent with the observations.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-232392 (URN)10.1103/PhysRevFluids.3.074201 (DOI)000437675700001 ()2-s2.0-85051108122 (Scopus ID)
Funder
EU, European Research Council, 258980Swedish Research Council, 2014-04505
Note

QC 20180726

Available from: 2018-07-26 Created: 2018-07-26 Last updated: 2020-03-23Bibliographically approved
Lindahl, V., Gourdon, P., Andersson, M. & Hess, B. (2018). Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function. Scientific Reports, 8, Article ID 2995.
Open this publication in new window or tab >>Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 2995Article in journal (Refereed) Published
Abstract [en]

Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-223791 (URN)10.1038/s41598-018-21357-2 (DOI)000424985800033 ()29445244 (PubMedID)2-s2.0-85042110483 (Scopus ID)
Funder
EU, European Research Council, 258980Swedish Research Council, 2014-4505Swedish e‐Science Research Center
Note

QC 20180307

Available from: 2018-03-07 Created: 2018-03-07 Last updated: 2018-03-07Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2018). Riemann metric approach to optimal sampling of multidimensional free-energy landscapes. Physical review. E, 98(2), Article ID 023312.
Open this publication in new window or tab >>Riemann metric approach to optimal sampling of multidimensional free-energy landscapes
2018 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 2, article id 023312Article in journal (Refereed) Published
Abstract [en]

Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%-70%.

Place, publisher, year, edition, pages
American Physical Society, 2018
Keywords
Bioinformatics, Boltzmann equation, Computational chemistry, Mathematical transformations, Molecular dynamics, Reaction kinetics, Boltzmann distribution, Computational overheads, Conformational transitions, Free-energy calculations, High-dimensional models, Molecular dynamics simulations, Multidimensional free energy, Nonlinear coordinate transformation, Free energy
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-236741 (URN)10.1103/PhysRevE.98.023312 (DOI)000443145500007 ()30253489 (PubMedID)2-s2.0-85052735453 (Scopus ID)
Note

Export Date: 22 October 2018; Article; Correspondence Address: Hess, B.; Department of Physics, Swedish E-Science Research Center, KTH Royal Institute of TechnologySweden; email: hess@kth.se; Funding details: HPC2N; Funding details: SNIC 2016/10-47; Funding details: 2017/11-25; Funding details: 2016/1-562; Funding details: 258980, ERC, European Research Council; Funding details: 2014-4505, VR, Vetenskapsrådet; Funding text: This research was supported by the European Research Council (grant no. 258980) and the Swedish Research Council (grant no. 2014-4505). The simulations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC 2016/1-562, SNIC 2016/10-47, and 2017/11-25) at the PDC Centre for High Performance Computing (PDC-HPC) and the High Performance Computing Center North (HPC2N). QC 20181022

Available from: 2018-10-22 Created: 2018-10-22 Last updated: 2020-03-09Bibliographically approved
Kohnke, B., Ullmann, R. T., Kutzner, C., Beckmann, A., Haensel, D., Kabadshow, I., . . . Grubmueller, H. (2017). A Flexible, GPU - Powered Fast Multipole Method for Realistic Biomolecular Simulations in Gromacs. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 112(3), 448A-448A
Open this publication in new window or tab >>A Flexible, GPU - Powered Fast Multipole Method for Realistic Biomolecular Simulations in Gromacs
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2017 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 448A-448AArticle in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
Cell Press, 2017
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-269605 (URN)10.1016/j.bpj.2016.11.2402 (DOI)000402375700212 ()
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Note

QC 20200310

Available from: 2020-03-10 Created: 2020-03-10 Last updated: 2020-03-10Bibliographically approved
Wennberg, C. L., Murtola, T., Pall, S., Abraham, M. J., Hess, B. & Lindahl, E. (2015). Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation. Journal of Chemical Theory and Computation, 11(12), 5737-5746
Open this publication in new window or tab >>Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation
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2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 12, p. 5737-5746Article in journal (Refereed) Published
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
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-180232 (URN)10.1021/acs.jctc.5b00726 (DOI)000366223400017 ()26587968 (PubMedID)2-s2.0-84949640540 (Scopus ID)
Note

QC 20160119

Available from: 2016-01-19 Created: 2016-01-08 Last updated: 2017-11-30Bibliographically approved
Abraham, M. J., Murtola, T., Schulz, R., Pall, S., Smith, J. C., Hess, B. & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19-25
Open this publication in new window or tab >>GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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2015 (English)In: SoftwareX, E-ISSN 2352-7110, Vol. 1-2, p. 19-25Article in journal (Refereed) Published
Abstract [en]

GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
Molecular dynamics, GPU, SIMD, Free energy
National Category
Physical Sciences
Research subject
Chemistry
Identifiers
urn:nbn:se:kth:diva-248468 (URN)10.1016/j.softx.2015.06.001 (DOI)2-s2.0-84946416234 (Scopus ID)
Note

QC 20190429

Available from: 2019-04-09 Created: 2019-04-09 Last updated: 2019-04-29Bibliographically approved
Ullmann, R. T., Kutzner, C., Beckmann, A., Kohnke, B., Kabadashow, I., Dachsel, H., . . . Grubmueller, H. (2015). GromEx: Electrostatics with chemical variability for realistic molecular simulations on the exascale. Paper presented at 10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY. European Biophysics Journal, 44, S145-S145
Open this publication in new window or tab >>GromEx: Electrostatics with chemical variability for realistic molecular simulations on the exascale
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2015 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S145-S145Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER, 2015
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-243670 (URN)000380001400391 ()
Conference
10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY
Note

QC 20190304

Available from: 2019-03-04 Created: 2019-03-04 Last updated: 2019-03-04Bibliographically approved
Lindahl, V., Lidmar, J. & Hess, B. (2015). Sampling rare biomolecular events with adaptive pulling simulations. Paper presented at 10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY. European Biophysics Journal, 44, S144-S144
Open this publication in new window or tab >>Sampling rare biomolecular events with adaptive pulling simulations
2015 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S144-S144Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
SPRINGER, 2015
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-243669 (URN)000380001400390 ()
Conference
10th European-Biophysical-Societies-Association (EBSA) European Biophysics Congress, JUL 18-22, 2015, Dresden, GERMANY
Note

QC 20190304

Available from: 2019-03-04 Created: 2019-03-04 Last updated: 2019-05-20Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7498-7763

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