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  • 1.
    Abraham, Mark J
    Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, Australia.
    Performance enhancements for GROMACS nonbonded interactions on BlueGene.2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.

  • 2.
    Abraham, Mark J
    et al.
    Australian National University, Australia.
    Gready, Jill E
    Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.52011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed)
    Abstract [en]

    Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

  • 3.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Basis set dependence of solute-solvent interaction energy of benzene in water: a HF/DFT study2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 11, p. 1725-1732Article in journal (Refereed)
    Abstract [en]

    Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.

  • 4.
    Bondesson, Laban
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Royal Inst Technol, Dept Theoret Chem, SE-10691 Stockholm, Sweden..
    Erratum to: Basis set dependence of solute-solvent interaction energy of benzene in waterA HF/DFT study (vol 29, pg 1725, 2008)2012In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, no 3, p. 354-354Article in journal (Refereed)
  • 5. Cordomi, Arnau
    et al.
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Perez, Juan J.
    Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 6, p. 1017-1030Article, review/survey (Refereed)
    Abstract [en]

    The present study analyzes the effect of the simulation conditions on the results of molecular dynamics simulations of G-protein coupled receptors (GPCRs) performed with an explicit lipid bilayer. Accordingly, the present work reports the analysis of different simulations of bovine rhodopsin embedded in a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer using two different sampling conditions and two different approaches for the treatment of long-range electrostatic interactions. Specifically, sampling was carried out either by using the statistical ensembles NVT or NPT (constant number of atoms, a pressure of 1 arm in all directions and fixed temperature), and the electrostatic interactions were treated either by using a twin-cutoff, or the particle mesh Ewald summation method (PME). The results of the present study suggest that the use of the NPT ensemble in combination with the PME method provide more realistic simulations. The use of NPT during the equilibration avoids the need of an a priori estimation of the box dimensions, giving the correct area per lipid. However, once the system is equilibrated, the simulations are irrespective of the sampling conditions used. The use of an electrostatic cutoff induces artifacts on both lipid thickness and the ion distribution, but has no direct effect on the protein and water molecules.

  • 6. Ding, Zongling
    et al.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Xing, Huaizhong
    Shu, Haibo
    Dong, Ruibin
    Chen, Xiaoshuang
    Lu, Wei
    Transport Properties of Graphene Nanoribbon-Based Molecular Devices2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 4, p. 737-741Article in journal (Refereed)
    Abstract [en]

    The electronic and transport properties of an edge-modified prototype graphene nanoribbon (GNR) slice are investigated using density functional theory and Green's function theory. Two decorating functional group pairs are considered, such as hydrogen-hydrogen and NH2-NO2 with NO2 and NH2 serving as a donor and an acceptor, respectively. The molecular junctions consist of carbon-based GNR slices sandwiched between Au electrodes. Nonlinear I-V curves and quantum conductance have been found in all the junctions. With increasing the source-drain bias, the enhancement of conductance is quantized. Several key factors determining the transport properties such as the electron transmission probabilities, the density of states, and the component of Frontier molecular orbitals have been discussed in detail. It has been shown that the transport properties are sensitive to the edge type of carbon atoms. We have also found that the accepter-donor functional pairs can cause orders of magnitude changes of the conductance in the junctions.

  • 7. Ding, Zongling
    et al.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Xing, Huaizhong
    Shu, Haibo
    Huang, Yan
    Chen, Xiaoshuang
    Lu, Wei
    The Finite-Size Effect on the Transport Properties in Edge-Modified Graphene Nanoribbon-Based Molecular Devices2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 8, p. 1753-1759Article in journal (Refereed)
    Abstract [en]

    The size-dependence on the electronic and transport properties of the molecular devices of the edge-modified graphene nanoribbon (GNR) slices is investigated using density-functional theory and Green's function theory. Two edge-modifying functional group pairs are considered. Energy gap is found in all the GNR slices. The gap shows an exponential decrease with increasing the slice size of two vertical orientations in the two edge terminated cases, respectively. The tunneling probability and the number of conducting channel decreases with increasing the GNR-slices size in the junctions. The results indicate that the acceptor-donor pair edge modulation can improve the quantum conductance and decrease the finite-size effect on the transmission capability of the GNR slice-based molecular devices.

  • 8. Eriksen, Janus J.
    et al.
    Olsen, Jogvan Magnus H.
    Aidas, Kestutis
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, Kurt V.
    Kongsted, Jacob
    Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 13, p. 2853-2864Article in journal (Refereed)
    Abstract [en]

    In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.

  • 9.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Roca-Sanjuan, Daniel
    Aquilante, Francesco
    A Two-Scale Approach to Electron Correlationin Multiconfigurational Perturbation Theory2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, p. 1609-1617Article in journal (Refereed)
    Abstract [en]

    We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environmentis meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposedscheme represent a hierarchical approach to the electroncorrelation problem, where two molecular scales aretreated each by means of the most suitable level of theory.

  • 10.
    Gao, Bin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liu, Kai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wu, Ziyu
    Chinese Acad Sci, Inst High Energy Phys, Beijing.
    Lu, Wei
    Chinese Acad Sci, Natl Lab Infrared Phys, Shanghai Inst Tech Phys, Beijing.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    An efficient first-principle approach for electronic structures calculations of nanomaterials2008In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 29, no 3, p. 434-444Article in journal (Refereed)
    Abstract [en]

    An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.

  • 11.
    Georgieva, Polina
    et al.
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Himo, Fahmi
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Quantum Chemical Modeling of Enzymatic Reactions: The Case of Histone Lysine Methyltransferase2010In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 31, no 8, p. 1707-1714Article in journal (Refereed)
    Abstract [en]

    Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.

  • 12.
    Hugosson, Håkan Wilhelm
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Laio, A.
    Maurer, P.
    Rothlisberger, U.
    A comparative theoretical study of dipeptide solvation in water2006In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 27, no 5, p. 672-684Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus oil the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but call differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins, with charged -NH3+ and -CO2- side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He. 71.15.Pd).

  • 13. Kikugawa, Gota
    et al.
    Apostolov, Rossen
    Osaka University.
    Kamiya, Narutoshi
    Taiji, Makoto
    Himeno, Ryutaro
    Nakamura, Haruki
    Yonezawa, Yasushige
    Application of MDGRAPE-3, a Special Purpose Board for Molecular Dynamics Simulations, to Periodic Biomolecular Systems2009In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 30, no 1, p. 110-118Article in journal (Refereed)
    Abstract [en]

    We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.

  • 14. Kutzner, Carsten
    et al.
    Pall, Szilard
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Fechner, Martin
    Esztermann, Ansgar
    de Groot, Bert L.
    Grubmueller, Helmut
    Best bang for your buck: GPU nodes for GROMACS biomolecular simulations2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 26, p. 1990-2008Article in journal (Refereed)
    Abstract [en]

    The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off-loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.

  • 15.
    Kutzner, Carsten
    et al.
    Max Planck Inst Biophys Chem, Theoret & Computat Biophys, Fassberg 11, D-37077 Gottingen, Germany. al$$$l, Szilard.
    Páll, Szilard
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Fechner, Martin
    Esztermann, Ansgar
    de Groot, Bert L.
    Grubmüller, Helmut
    More bang for your buck: Improved use of GPU nodes for GROMACS 20182019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987XArticle in journal (Refereed)
    Abstract [en]

    We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more toward the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift toward GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware.

  • 16.
    Kutzner, Carsten
    et al.
    Max-Planck Institut Göttingen.
    van der Spoel, David
    Uppsala University.
    Fechner, Martin
    Max-Planck Institut Göttingen.
    Lindahl, Erik
    Stockholm University.
    Schmitt, Udo W
    Max-Planck Institut Göttingen.
    de Groot, Bert L
    Max-Planck Institut Göttingen.
    Grubmüller, Helmut
    Max-Planck Institut Göttingen.
    Software news and update: Speeding up parallel GROMACS on high-latency networks2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 12, p. 2075-84Article in journal (Refereed)
    Abstract [en]

    We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high single-node performance of GROMACS, however, on the widely used Ethernet switched clusters, the scaling typically breaks down when more than two computer nodes are involved, limiting the absolute speedup that can be gained to about 3 relative to a single-CPU run. With the LAM MPI implementation, the main scaling bottleneck is here identified to be the all-to-all communication which is required every time step. During such an all-to-all communication step, a huge amount of messages floods the network, and as a result many TCP packets are lost. We show that Ethernet flow control prevents network congestion and leads to substantial scaling improvements. For 16 CPUs, e.g., a speedup of 11 has been achieved. However, for more nodes this mechanism also fails. Having optimized an all-to-all routine, which sends the data in an ordered fashion, we show that it is possible to completely prevent packet loss for any number of multi-CPU nodes. Thus, the GROMACS scaling dramatically improves, even for switches that lack flow control. In addition, for the common HP ProCurve 2848 switch we find that for optimum all-to-all performance it is essential how the nodes are connected to the switch's ports. This is also demonstrated for the example of the Car-Parinello MD code.

  • 17.
    Larsson, Per
    et al.
    Stockholm University, Sweden.
    Lindahl, Erik
    Stockholm University, Sweden.
    A High-Performance Parallel-Generalized Born Implementation Enabled by Tabulated Interaction Rescaling2010In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 31, no 14, p. 2593-2600Article in journal (Refereed)
    Abstract [en]

    Implicit solvent representations, in general, and generalized Born models, in particular, provide an attractive way to reduce the number of interactions and degrees of freedom in a system. The instantaneous relaxation of the dielectric shielding provided by an implicit solvent model can be extremely efficient for high-throughput and Monte Carlo studies, and a reduced system size can also remove a lot of statistical noise. Despite these advantages, it has been difficult for generalized Born implementations to significantly outperform optimized explicit-water simulations due to more complex functional forms and the two extra interaction stages necessary to calculate Born radii and the derivative chain rule terms contributing to the force. Here, we present a method that uses a rescaling transformation to make the standard generalized Born expression a function of a single variable, which enables an efficient tabulated implementation on any modern CPU hardware. The total performance is within a factor 2 of simulations in vacuo. The algorithm has been implemented in Gromacs, including single-instruction multiple-data acceleration, for three different Born radius models and corresponding chain rule terms. We have also adapted the model to work with the virtual interaction sites commonly used for hydrogens to enable long-time steps, which makes it possible to achieve a simulation performance of 0.86 micros/day for BBA5 with 1-nm cutoff on a single quad-core desktop processor. Finally, we have also implemented a set of streaming kernels without neighborlists to accelerate the non-cutoff setup occasionally used for implicit solvent simulations of small systems.

  • 18.
    Lousada, Claudio M.
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Materials Technology.
    Korzhavyi, Pavel A.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Materials Technology.
    Surface Chemistry of Oxygen on Aluminum-Performance of the Density Functionals: PBE, PBE0, M06, and M06-L2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 9, p. 787-794Article in journal (Refereed)
    Abstract [en]

    We investigated the performance of the density functional theory (DFT) functionals PBE, PBE0, M06, and M06-L for describing the molecular and dissociative adsorption of O2 onto pure and doped Al(111) surfaces. Adsorption of O2 was studied at the perfect Al(111) surface and compared with the case where an additional Al atom was present as an adatom. Additionally, we studied how these functionals perform when different dopants are present at the Al(111) surface in two distinct geometries: as an adatom or as a substitutional atom replacing an Al atom. The performance of the different functionals is greatly affected by the surface geometry. The inclusion of Hartree-Fock exchange in the functional leads to slight differences in adsorption energies for molecular adsorption of O2. These differences become very pronounced for dissociative adsorption, with the hybrids PBE0 and M06 predicting more exergonic adsorption than PBE and M06-L. Furthermore, PBE0 and M06 predicted trends in adsorption energies for defective and perfect surfaces which are in line with the experimental knowledge of the effects of surface defects in adsorption energies. The predictions of the non-hybrids PBE and M06-L point in the opposite direction. The analysis of the contributions of the van der Waals (vdW) forces to the adsorption energies reveals that the PBE and PBE0 functionals have similar difficulties in describing vdW interactions for molecular adsorption of O2 while the M06 functional can give a description of these forces with an accuracy which is at least similar to that of the correction of the D3 type.

  • 19.
    Lundborg, Magnus
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Apostolov, Rossen
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Spångberg, Daniel
    Gärdenäs, Anders
    van der Spoel, David
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, no 3, p. 260-269Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.

  • 20.
    Nakagawa, Setsuko
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Polarizable model potential function for nucleic acid bases2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 9, p. 1538-1550Article in journal (Refereed)
    Abstract [en]

    A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G(2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.

  • 21.
    Pei, Han-Wen
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.). Stockholm Univ, Arrhenius Lab, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.
    Laaksonen, Aatto
    Stockholm Univ, Arrhenius Lab, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.;Nanjing Tech Univ, State Key Lab Mat Oriented & Chem Engn, Nanjing 210009, Jiangsu, Peoples R China.;Petru Poni Inst Macromol Chem, Ctr Adv Res Bionanoconjugates & Biopolymers, Aleea Grigore Ghica Voda 41A, Iasi 700487, Romania..
    Feature vector clustering molecular pairs in computer simulations2019In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987XArticle in journal (Refereed)
    Abstract [en]

    A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P-6,P-6,P-6,P-14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109-118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094-1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. 2

  • 22.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 16, p. 2531-2537Article in journal (Refereed)
    Abstract [en]

    A hierarchic sparse matrix data structure for Hartree-Fock/Kohn-Sham calculations is presented. The data structure makes the implementation of matrix manipulations needed for large systems faster, easier, and more maintainable without loss of performance. Algorithms for symmetric matrix square and inverse Cholesky decomposition within the hierarchic framework are also described. The presented data structure is general; in addition to its use in HartreeFock/Kohn-Sham calculations, it may also be used in other research areas where matrices with similar properties are encountered. The applicability of the data structure to ab initio calculations is shown with help of benchmarks on water droplets and graphene nanoribbons.

  • 23.
    Rubensson, Emanuel H.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rudberg, Elias
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Truncation of Small Matrix Elements Based on the Euclidean Norm for Blocked Data Structures2009In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 30, no 6, p. 974-977Article in journal (Refereed)
    Abstract [en]

    Methods for the removal of small symmetric matrix elements based on the Euclidean norm of the error matrix are presented in this article. In large scale Hartree-Fock and Kohn-Sham calculations it is important to be able to enforce matrix sparsity while keeping errors under control. Truncation based on some unitary-invariant norm allows for control of errors in the occupied subspace as described in (Rubensson et al. J Math Phys 49, 032103). The Euclidean norm is unitary-invariant and does not grow intrinsically with system size and is thus suitable for error control in large scale calculations. The presented truncation schemes repetitively use the Lanczos method to compute the Euclidean norms of the error matrix candidates. Ritz value convergence patterns are utilized to reduce the total number of Lanczos iterations.

  • 24.
    Rubensson, Emanuel
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Systematic sparse matrix error control for linear scaling electronic structure calculations2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 15, p. 1628-1637Article in journal (Refereed)
    Abstract [en]

     Efficient truncation criteria used in multiatom blocked sparse matrix operations for ab initio calculations are proposed. As system size increases, so does the need to stay on top of errors and still achieve high performance. A variant of a blocked sparse matrix algebra to achieve strict error control with good performance is proposed. The presented idea is that the condition to drop a certain submatrix should depend not only on the magnitude of that particular submatrix, but also on which other submatrices that are dropped. The decision to remove a certain submatrix is based on the contribution the removal would cause to the error in the chosen norm. We study the effect of an accumulated truncation error in iterative algorithms like trace correcting density matrix purification. One way to reduce the initial exponential growth of this error is presented. The presented error control for a sparse blocked matrix toolbox allows for achieving optimal performance by performing only necessary operations needed to maintain the requested level of accuracy.

  • 25.
    Salek, Pawel
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Hesselmann, Andreas
    A self-contained and portable density functional theory library for use in ab initio quantum chemistry programs2007In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 28, no 16, p. 2569-2575Article in journal (Refereed)
    Abstract [en]

    A major unresolved problem of density functional theory is the yet unknown exchange-correlation functional, which leads to a proliferation of its less or more successful approximations. A practical implementation of these numerous functionals can present a substantial challenge particularly if the higher order functional derivatives are required. We present a systematic method of functional implementation. The method allows a clean handling of a large number of functionals in a mutually independent way. We developed an extensive set of automatic test routines to facilitate functional and derivative testing with respect to the implementation correctness and numerical stability. An integral part of the presented solution is a program for automatic code generation from analytical formulas that uses only freely available tools. Code for evaluation of functionals and their first, second, third, and fourth derivatives can be generated, which accelerates the development, implementation, and testing of new functionals.

  • 26. Sun, C.
    et al.
    Zhu, L.
    Zhang, C.
    Song, Ce
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China, Hefei, Anhui, China.
    Wang, C.
    Zhang, M.
    Xie, Y.
    Schaefer, H. F. , I I I
    Conformers, properties, and docking mechanism of the anticancer drug docetaxel: DFT and molecular dynamics studies2018In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 39, no 15, p. 889-900Article in journal (Refereed)
    Abstract [en]

    The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single-bond rotamers and screened with the B3LYP/3-21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6-311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single-point relative energies were then determined at the M06-L/6-311G(2df,p) level. The UV spectrum of the lowest-lying DTX conformer in methanol was investigated with the TD-CAM-B3LYP/6-311 + G(2df,p) method. The 31 unique DTX structures are mainly docked at three different sites within β-tubulin. Based on the results of molecular docking and double-float MD simulations, the lowest-lying DTX conformer consistently exhibits good docking performance with β-tubulin. We identified the residues LYS299, ARG215, GLN294, LEU275, THR216, GLU290, PRO274, and THR276 on β-tubulin as active sites forming a binding pocket responsible for locking DTX within β-tubulin to make the combination more stable. The RMSD values show that the predicted complexes are favorable, and the SASA analysis shows that the hydrophilic properties of DTX are better than paclitaxel.

  • 27.
    Van Der Spoel, David
    et al.
    Uppsala University.
    Lindahl, Erik
    Stockholm University.
    Hess, Berk
    Max-Planck Institut Mainz.
    Groenhof, Gerrit
    Max-Planck Institut Göttingen.
    Mark, Alan E.
    Groningen University.
    Berendsen, Herman J. C.
    Groningen University.
    GROMACS: fast, flexible, and free2005In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 26, no 16, p. 1701-1718Article in journal (Refereed)
    Abstract [en]

    This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

  • 28. Witzke, Sarah
    et al.
    Holmgaard List, Nanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Olsen, Jogvan Magnus Haugaard
    Steinmann, Casper
    Petersen, Michael
    Beerepoot, Maarten T. P.
    Kongsted, Jacob
    An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes2017In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 38, no 9, p. 601-611Article in journal (Refereed)
    Abstract [en]

    A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoylsn- glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies.

  • 29. Yang, Sheng-Chun
    et al.
    Wang, Yong-Lei
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.). KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Jiao, Gui-Sheng
    Qian, Hu-Jun
    Lu, Zhong-Yuan
    Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non-uniform fast fourier transform2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 3, p. 378-387Article in journal (Refereed)
    Abstract [en]

    We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new algorithm is developed for NFFT for the evaluations of electrostatic interaction energies and forces. Both real-space and reciprocal-space computations are further accelerated by using graphical processing units (GPU) with CUDA technology. Especially, the use of CUNFFT (NFFT based on CUDA) very much reduces the reciprocal-space computation. In order to reach the best performance of this method, we propose a procedure for the selection of optimal parameters with controlled accuracies. With the choice of suitable parameters, we show that our method is a good alternative to the standard Ewald method with the same computational precision but a dramatically higher computational efficiency.

  • 30.
    Zaleśny, Robert
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Hättig, C.
    Bartkowiak, W.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline2015In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 15, p. 1124-1131Article in journal (Refereed)
    Abstract [en]

    In this study, we predict vibronic two-photon absorption (TPA) spectra for 4-nitroaniline in vacuo. The simulations are performed using density functional theory and the approximate second-order coupled-cluster singles and doubles model CC2. Thereby we also demonstrate the possibility of simulations of vibronic TPA spectra with ab initio wavefunction methods that include electron correlation for medium-sized systems. A special focus is put on the geometric derivatives of the second-order transition moment and the dipole moment difference between the charge-transfer excited state and the ground state. The results of CC2 calculations bring new insight into the vibronic coupling mechanism in TPA spectra of 4-nitroniline and demonstrate that the mixed term is quite large and that it also exhibits a negative interference with the Franck-Condon contribution. CC2 method and several exchange-correlation functionals are used to predict vibronic two-photon absorption spectra of 4-nitroaniline.

  • 31.
    Zhang, Igor Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Jianming
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xu, Xin
    Accurate Bond Dissociation Enthalpies by Using Doubly Hybrid XYG3 Functional2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9, p. 1824-1838Article in journal (Refereed)
    Abstract [en]

    In this work, we examine the performance of XYG3, a newly developed doubly hybrid density functional (Zhang, Xu, and Goddard III, Proc Natl Acad Sci USA 2009, 106, 4963), to calculate covalent bond dissociation enthalpy (BDE). We use 5 atoms, 32 molecular radicals, and 116 closed-shell molecules to set up 142 bond dissociation reactions. For the total of 148 heats of formation (HOFs) and 142 BDEs, XYG3 leads to mean absolute deviations (MADs) of 1.45 and 1.87 kcal/mol, respectively. In comparison with some other functionals, MADs for HOFs are 2.31 (M06-2X), 2.98 (B2PLYP-D), 3.04 (BMK), 3.96 (B3LYP), 4.47 (B2PLYP), 5.42 (B2GP-PLYP), 6.46 (PBE0), and 29.93 kcal/mol (B3P86), and the corresponding errors for BDEs are 2.06 (M06-2X), 2.25 (BMK), 2.51 (B2PLYP-D), 2.89 (B2GP-PLYP), 3.30 (B3P86), 3.44 (B2PLYP), 3.87 (PBE0), and 6.14 kcal/mol (B3LYP). (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 1824-1838, 2011

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