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Van der Spoel, David
Publications (10 of 108) Show all publications
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 and Systems Biology
Identifiers
urn:nbn:se:uu:diva-377803 (URN)10.1371/journal.pcbi.1006649 (DOI)000457372500019 ()30653494 (PubMedID)
Available from: 2019-02-27 Created: 2019-02-27 Last updated: 2019-02-27Bibliographically approved
Zhang, H., Yin, C., Jiang, Y. & van der Spoel, D. (2018). Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. Journal of Chemical Information and Modeling, 58(5), 1037-1052
Open this publication in new window or tab >>Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models
2018 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 58, no 5, p. 1037-1052Article in journal (Refereed) Published
Abstract [en]

Thermodynamic and kinetic properties are of critical importance for the applicability of computational models to biomolecules such as proteins. Here we present an extensive evaluation of the Amber ff99SB-ILDN force field for modeling of hydration and diffusion of amino acids with three-site (SPC, SPC/E, SPC/E-b , and TIP3P), four-site (TIP4P, TIP4P-Ew, and TIP4P/2005), and five-site (TIPSP and TIP5P-Ew) water models. Hydration free energies (HFEs) of neutral amino acid side chain analogues have little dependence on the water model, with a root-mean-square error (RMSE) of similar to 1 kcal/mol from experimental observations. On the basis of the number of interacting sites in the water model, HFEs of charged side chains can be putatively classified into three groups, of which the group of three-site models lies between those of four- and five-site water models; for each group, the water model dependence is greatly eliminated when the solvent Galvani potential is considered. Some discrepancies in the location of the first hydration peak (R-RDF) in the ion-water radial distribution function between experimental and calculated observations were detected, such as a systematic underestimation of the acetate (Asp side chain) ion. The RMSE of calculated diffusion coefficients of amino acids from experiment increases linearly with the increasing diffusion coefficients of the solvent water models at infinite dilution. TIP3P has the fastest diffusivity, in line with literature findings, while the "FB" and "OPC" water model families as well as TIP4P/2005 perform well, within a relative error of 5%, and TIP4P/2005 yields the most accurate estimate for the water diffusion coefficient. All of the tested water models overestimate amino acid diffusion coefficients by approximately 40% (TIP4P/2005) to 200% (TIP3P). Scaling of protein-water interactions with TIP4P/2005 in the Amber ff99SBws and ff03ws force fields leads to more negative HFEs but has little influence on the diffusion of amino acids. The most recent FF/water combinations of ff14SB/OPC3, ffl5ipq/SPC/E-b, and fb15/TIP3P-FB do not show obvious improvements in accuracy for the tested quantities. These findings here establish a benchmark that may aid in the development and improvement of classical force fields to accurately model protein dynamics and thermodynamics.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-357575 (URN)10.1021/acs.jcim.8b00026 (DOI)000433634900013 ()29648448 (PubMedID)
Funder
Swedish Research Council, 2013-5947
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Bashardanesh, Z. & van der Spoel, D. (2018). Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids. Journal of Physical Chemistry B, 122(33), 8018-8027
Open this publication in new window or tab >>Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids
2018 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 33, p. 8018-8027Article in journal (Refereed) Published
Abstract [en]

In the context of studies of proteins under crowding conditions, it was found that there is a tendency of simulated proteins to coagulate in a seemingly unphysical manner. This points to an imbalance in the protein-protein or protein-water interactions. One way to resolve this is to strengthen the protein-water Lennard-Jones interactions. However, it has also been suggested that dispersion interactions may have been systematically overestimated in force fields due to parameterization with a short cutoff. Here, we test this proposition by performing simulations of liquids and of proteins in solution with systematically reduced C-6 (dispersion constant in a 12-6 Lennard-Jones potential) and evaluate the properties. We find that simulations of liquids with either a dispersion correction or explicit long-range Lennard-Jones interactions need little or no correction to the dispersion constant to reproduce the experimental density. For simulations of proteins, a significant reduction in the dispersion constant is needed to reduce the coagulation, however. Because the protein- and liquid force fields share atom types, at least to some extent, another solution for the coagulation problem may be needed, either through including explicit polarization or through strengthening protein-water interactions.

National Category
Physical Chemistry Biophysics
Identifiers
urn:nbn:se:uu:diva-364048 (URN)10.1021/acs.jpcb.8b05770 (DOI)000442959900008 ()30084244 (PubMedID)
Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2018-12-10Bibliographically approved
Fischer, N. M., Poleto, M. D., Steuer, J. & van der Spoel, D. (2018). Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations. Nucleic Acids Research, 46(10), 4872-4882
Open this publication in new window or tab >>Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
2018 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 10, p. 4872-4882Article in journal (Refereed) Published
Abstract [en]

The structure of ribonucleic acid (RNA) polymers is strongly dependent on the presence of, in particular Mg2+ cations to stabilize structural features. Only in high-resolution X-ray crystallography structures can ions be identified reliably. Here, we perform molecular dynamics simulations of 24 RNA structures with varying ion concentrations. Twelve of the structures were helical and the others complex folded. The aim of the study is to predict ion positions but also to evaluate the impact of different types of ions (Na+ or Mg2+) and the ionic strength on structural stability and variations of RNA. As a general conclusion Mg2+ is found to conserve the experimental structure better than Na+ and, where experimental ion positions are available, they can be reproduced with reasonable accuracy. If a large surplus of ions is present the added electrostatic screening makes prediction of binding-sites less reproducible. Distinct differences in ion-binding between helical and complex folded structures are found. The strength of binding (Delta G(+) for breaking RNA atom-ion interactions) is found to differ between roughly 10 and 26 kJ/mol for the different RNA atoms. Differences in stability between helical and complex folded structures and of the influence of metal ions on either are discussed.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2018
National Category
Structural Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-360542 (URN)10.1093/nar/gky221 (DOI)000438329100009 ()29718375 (PubMedID)
Funder
Swedish Research Council, 2013-5947eSSENCE - An eScience CollaborationSwedish National Infrastructure for Computing (SNIC), SNIC2016/34-44
Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20Bibliographically approved
Walz, M.-M., Ghahremanpour, M. M., van Maaren, P. J. & Van der Spoel, D. (2018). Phase-Transferable Force Field for Alkali Halides. Journal of Chemical Theory and Computation, 14(11), 5933-5948
Open this publication in new window or tab >>Phase-Transferable Force Field for Alkali Halides
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 11, p. 5933-5948Article in journal (Refereed) Published
Abstract [en]

A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet been created. Progress toward this goal has been limited, as most work has concentrated on just one phase, often determined by particular applications. In the framework of the development of the Alexandria force field, we present here new polarizable force fields for alkali halides with Gaussian charge distributions for molecular dynamics simulations. We explore different descriptions of the van der Waals interaction, like the commonly applied 12-6 Lennard-Jones (LJ), and compare it to "softer" ones, such as the 8-6 LJ, Buckingham, and a modified Buckingham potential. Our results for physicochemical properties of the gas, liquid, and solid phases of alkali halides are compared to experimental data and calculations with reference polarizable and nonpolarizable force fields. The new polarizable force field that employs a modified Buckingham potential predicts the tested properties for gas, liquid, and solid phases with a very good accuracy. In contrast to reference force fields, this model reproduces the correct crystal structures for all alkali halides at low and high temperature. Seeing that experiments with molten salts may be tedious due to high temperatures and their corrosive nature, the models presented here can contribute significantly to our understanding of alkali halides in general and melts in particular.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-371549 (URN)10.1021/acs.jctc.8b00507 (DOI)000450695200042 ()30300552 (PubMedID)
Funder
Swedish Research Council, 2013-5947Swedish Research Council, SNIC2017-12-41eSSENCE - An eScience Collaboration
Available from: 2018-12-21 Created: 2018-12-21 Last updated: 2018-12-21Bibliographically approved
Walz, M.-M., Ghahremanpour, M. M., van Maaren, P. J. & Van der Spoel, D. (2018). Phase-Transferable Force Field for Alkali Halides. Journal of Chemical Theory and Computation
Open this publication in new window or tab >>Phase-Transferable Force Field for Alkali Halides
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380340 (URN)10.1021/acs.jctc.8b00507 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
Ghahremanpour, M. M., van Maaren, P. J., Caleman, C., Hutchison, G. R. & Van der Spoel, D. (2018). Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. Journal of Chemical Theory and Computation, 14(11), 5553-5566
Open this publication in new window or tab >>Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 11, p. 5553-5566Article in journal (Refereed) Published
Abstract [en]

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-371548 (URN)10.1021/acs.jctc.8b00430 (DOI)000450695200011 ()30281307 (PubMedID)
Funder
Swedish Research Council, 2013-5947Swedish Research Council, SNIC2016/34-44
Available from: 2018-12-21 Created: 2018-12-21 Last updated: 2018-12-21Bibliographically approved
Ghahremanpour, M. M., van Maaren, P. J., Caleman, C., Hutchison, G. R. & Van der Spoel, D. (2018). Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. Journal of Chemical Theory and Computation
Open this publication in new window or tab >>Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380336 (URN)10.1021/acs.jctc.8b00430 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
Van der Spoel, D., Ghahremanpour, M. M. & Lemkul, J. A. (2018). Small Molecule Thermochemistry: A Tool for Empirical Force Field Development. Journal of Physical Chemistry A, 122(45), 8982-8988
Open this publication in new window or tab >>Small Molecule Thermochemistry: A Tool for Empirical Force Field Development
2018 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 45, p. 8982-8988Article in journal (Refereed) Published
Abstract [en]

Spectroscopic analysis of compounds is typically combined with density functional theory, for instance, for assigning vibrational frequencies, limiting application to relatively small compounds. Accurate classical force fields could, in principle, complement these quantum-chemical tools. A relatively simple way to validate vibrational frequencies is by computing thermochemical properties. We present such a validation for over 1800 small molecules using the harmonic approximation. Two popular empirical force fields (GAFF and CGenFF) are compared to experimental data and results from Gaussian-4 quantum-chemical calculations. Frequency scaling factors of 1.035 (CGenFF) and 1.018 (GAFF) are derived from the zero-point energies. The force field calculations have larger deviation from experiment than the G4 method for standard entropy, but for heat capacity the results are comparable. For internal thermal energy and zero-point energy the deviations from G4 are relatively small. The work suggests that with some tuning force fields could indeed complement DFT in spectroscopical applications.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-371532 (URN)10.1021/acs.jpca.8b09867 (DOI)000451101200020 ()30362355 (PubMedID)
Funder
Swedish Research Council, 2013-5947
Available from: 2019-01-07 Created: 2019-01-07 Last updated: 2019-01-07Bibliographically approved
Van der Spoel, D., Ghahremanpour, M. M. & Lemkul, J. A. (2018). Small Molecule Thermochemistry: A Tool for Empirical Force Field Development. Journal of Physical Chemistry A
Open this publication in new window or tab >>Small Molecule Thermochemistry: A Tool for Empirical Force Field Development
2018 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380341 (URN)10.1021/acs.jpca.8b09867 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
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