pinecone/core-2020-05-10-deduplication huggingface dataset:
O(N) continuous electrostatics solvation energies calculation method for
  biomolecules simulations

We report a development of a new fast surface-based method for numerical
calculations of solvation energy of biomolecules with a large number of charged
groups. The procedure scales linearly with the system size both in time and
memory requirements, is only a few percent wrong for any molecular
configurations of arbitrary sizes, gives explicit value for the reaction field
potential at any point, provides both the solvation energy and its derivatives
suitable for Molecular Dynamics simulations. The method works well both for
large and small molecules and thus gives stable energy differences for
quantities such as solvation energies of molecular complex formation.Comment: 6 pages, 4 figures, more results, examples and references adde
Protein Side Chain Modeling with Orientation-Dependent  Atomic Force Fields Derived by Series Expansions

We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance-dependent energy functions (OSCAR-d) and side-chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conformations from non-native conformations, using a training set of 12,000 side chains for each residue type. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. Then, the OSCAR-d were multiplied by an orientation-dependent function to yield OSCAR-o. A total of 1087 parameters of the orientation-dependent energy functions (OSCAR-o) were optimized by maximizing the energy gap between the native conformation and subrotamers calculated as low energy by OSCARd. When OSCAR-o with optimized parameters were used to model side chain conformations simultaneously for 218 recently released protein structures, the prediction accuracies were 88.8% for v1, 79.7% for v1 1 2, 1.24 A ࠯verall root mean square deviation (RMSD), and 0.62 A ࠒMSD for core residues, respectively, compared with the next-best performing side-chain modeling program which achieved 86.6% for v1, 75.7% for v1 1 2, 1.40 A ࠯verall RMSD, and 0.86 A ࠒMSD for core residues, respectively. The continuous energy functions obtained in this study are suitable for gradient-based optimization techniques for protein structure refinement.Full Tex
Acceleration of a QM/MM-QMC simulation using GPU

We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only
the bottle-neck part of the calculation is replaced by CUDA subroutine and
performed on GPU. The performance on a (single core CPU + GPU) is compared with
that on a (single core CPU with double precision), getting 23.6 (11.0) times
faster calculations in single (double) precision treatments on GPU. The energy
deviation caused by the single precision treatment was found to be within the
accuracy required in the calculation, \sim 10^{-5} hartree. The accelerated
computational nodes mounting GPU are combined to form a hybrid MPI cluster on
which we confirmed the performance linearly scales to the number of nodes.Comment: 22 pages, 5 figures, accepted by J. Comput. Che
DynamO: A free O(N) general event-driven molecular-dynamics simulator

Molecular-dynamics algorithms for systems of particles interacting through
discrete or "hard" potentials are fundamentally different to the methods for
continuous or "soft" potential systems. Although many software packages have
been developed for continuous potential systems, software for discrete
potential systems based on event-driven algorithms are relatively scarce and
specialized. We present DynamO, a general event-driven simulation package which
displays the optimal O(N) asymptotic scaling of the computational cost with the
number of particles N, rather than the O(N log(N)) scaling found in most
standard algorithms. DynamO provides reference implementations of the best
available event-driven algorithms. These techniques allow the rapid simulation
of both complex and large (>10^6 particles) systems for long times. The
performance of the program is benchmarked for elastic hard sphere systems,
homogeneous cooling and sheared inelastic hard spheres, and equilibrium
Lennard-Jones fluids. This software and its documentation are distributed under
the GNU General Public license and can be freely downloaded from
http://marcusbannerman.co.uk/dynamo
Randomized tree construction algorithm to explore energy landscapes

We report in the present work a new method for exploring conformational energy landscapes.\ud
The method, called T-RRT, combines ideas from statistical physics and robot path planning\ud
algorithms. A search tree is constructed on the conformational space starting from a given state.\ud
The tree expansion is driven by a double strategy: on the one hand, it is naturally biased towards\ud
yet unexplored regions of the space; on the other, a Monte Carlo-like transition test guides the\ud
expansion toward energetically favorable regions. The balance between these two strategies is\ud
automatically achieved thanks to a self-tuning mechanism. The method is able to efficiently find\ud
both, energy minima and transition paths between them. As a proof of concept, the method is\ud
applied to two academic benchmarks and to the alanine dipeptide.Postprint (author’s final draft
MATCH: An atom‐typing toolset for molecular mechanics force fields

We introduce a toolset of program libraries collectively titled multipurpose atom‐typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern‐matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom‐type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment‐based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave‐one‐out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized. © 2011 Wiley Periodicals, Inc. J Comput Chem, 201
SPINE X: Improving Protein Secondary Structure Prediction by Multistep Learning Coupled with Prediction of Solvent Accessible Surface Area and Backbone Torsion Angles

Accurate prediction of protein secondary structure is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. The accuracy of ab initio secondary structure prediction from sequence, however, has only increased from around 77 to 80% over the past decade. Here, we developed a multistep neural-network algorithm by coupling secondary structure prediction with prediction of solvent accessibility and backbone torsion angles in an iterative manner. Our method called SPINE X was applied to a dataset of 2640 proteins (25% sequence identity cutoff ) previously built for the first version of SPINE and achieved a 82.0% accuracy based on 10-fold cross validation (Q3). Surpassing 81% accuracy by SPINE X is further confirmed by employing an independently built test dataset of 1833 protein chains, a recently built dataset of 1975 proteins and 117 CASP 9 targets (critical assessment of structure prediction techniques) with an accuracy of 81.3%, 82.3% and 81.8%, respectively. The prediction accuracy is further improved to 83.8% for the dataset of 2640 proteins if the DSSP assignment used above is replaced by a more consistent consensus secondary structure assignment method. Comparison to the popular PSIPRED and CASP-winning structure-prediction techniques is made. SPINE X predicts number of helices and sheets correctly for 21.0% of 1833 proteins, compared to 17.6% by PSIPRED. It further shows that SPINE X consistently makes more accurate prediction in helical residues (6%) without over prediction while PSIPRED makes more accurate prediction in coil residues (3-5%) and over predicts them by 7%. SPINE X Server and its training/test datasets are available at http://sparks.informatics.iupui.edu/Full Tex
Rigid-CLL: avoiding constant-distance computations in cell linked-lists algorithms

Many of the existing molecular simulation tools require the efficient identification of the set of nonbonded interacting atoms. This is necessary, for instance, to compute the energy values or the steric contacts between atoms. Cell linked-lists can be used to determine the pairs of atoms closer than a given cutoff distance in asymptotically optimal time. Despite this long-term optimality, many spurious distances are anyway computed with this method. Therefore, several improvements have been proposed, most of them aiming to refine the volume of influence for each atom. Here, we suggest a different improvement strategy based on avoiding to fill cells with those atoms that are always at a constant distance of a given atom. This technique is particularly effective when large groups of the particles in the simulation behave as rigid bodies as it is the case in simplified models considering only few of the degrees of freedom of the molecule. In these cases, the proposed technique can reduce the number of distance computations by more than one order of magnitude, as compared with the standard cell linked-list technique. The benefits of this technique are obtained without incurring in additional computation costs, because it carries out the same operations as the standard cell linked-list algorithm, although in a different order. Since the focus of the technique is the order of the operations, it might be combined with existing improvements based on bounding the volume of influence for each atomPeer ReviewedPostprint (author’s final draft
Benchmarking the Thermodynamic Analysis of Water Molecules Around a Model Beta Sheet

Water molecules play a vital role in biological and engineered systems by controlling intermolecular interactions in the aqueous phase. Inhomogeneous fluid solvation theory provides a method to quantify solvent thermodynamics from molecular dynamics or Monte Carlo simulations and provides an insight into intermolecular interactions. In this study, simulations of TIP4P-2005 and TIP5P-Ewald water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. This allows the method to be benchmarked and provides information about the effect of a protein on the thermodynamics of nearby water molecules. The results show that the enthalpy converges with relatively little sampling, but the entropy and thus the free energy require considerably more sampling to converge. The two water models yield a very similar pattern of hydration sites, and these hydration sites have very similar thermodynamic properties, despite notable differences in their orientational preferences. The results also predict that a protein surface affects the free energy of water molecules to a distance of approximately 4.0 Å, which is in line with previous work. In addition, all hydration sites have a favorable free energy with respect to bulk water, but only when the water–water entropy term is included. A new technique for calculating this term is presented and its use is expected to be very important in accurately calculating solvent thermodynamics for quantitative application.Acknowledgements go to Mike Payne for careful reading of the manuscript, Stuart Rankin for technical help and the NVIDIA CUDA Centre of Excellence at the Cambridge HPCS for use of the CUDA-accelerated GPUs. All calculations were performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/) provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and were funded by the EPSRC under grant EP/F032773/1. Thanks for financial support go to the MRC, Wellcome Trust and EPSRC.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/jcc.2297
Extending Hirshfeld-I to bulk and periodic materials

In this work, a method is described to extend the iterative Hirshfeld-I
method, generally used for molecules, to periodic systems. The implementation
makes use of precalculated pseudo-potential based charge density distributions,
and it is shown that high quality results are obtained for both molecules and
solids, such as ceria, diamond, and graphite. The use of such grids makes the
implementation independent of the solid state or quantum chemical code used for
studying the system. The extension described here allows for easy calculation
of atomic charges and charge transfer in periodic and bulk systems.Comment: 11 pages, 4 Tables, 5 Figures, pre-referee draft only, much extended
  post referee version only available at publishe
Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation

The conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently\ud
developed in Dynamical Systems and also applied to Robotics, provide efficient algorithms to trace out implicitly defined sets. This paper describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this paper exploits the higher-dimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints.\ud
The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes.Preprin
Development of Direct Born–Oppenheimer Molecular Dynamics with Applications to Water Clusters and Mechanochemistry

New methods for Born-Oppenheimer molecular dynamics simulations have been developed and used to study protonated water clusters and mechanochemistry of alkanes. The novel algorithms are an efficient coordinate transformation and sampling microcanonical ensembles of trajectories used for generating starting conditions for simulations. In combination with existing techniques as well as with electronic structure methods within DALTON program, they make it a powerful tool to study reaction dynamics, free of charge.
This has been demonstrated by investigation of protonated water clusters relevant for water nucleation in atmospheric chemistry. The structure of the proton salvation shell and evaporation kinetics have been revealed.
Another application is the dynamics of alkanes under mechanical stress. Short-chain alkanes – butane and octane – are model compounds for polymers. Their dynamical behavior was simulated and analyzed under two scenarios mimicking the modes ofmechanochemical activation: slow stretching in the atomic-force microscope and violent action of ultrasound
Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models. However, their acceleration on parallel architectures such as Graphic Processing Units (GPU) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specic optimizations for CG models, such as dedicated data structures to handle dierent bead type interac- tions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three dierent GPU architectures as case studie
Reply to 'Comment on "Extending Hirshfeld-I to bulk and periodic
  materials" '

The issues raised in the comment by T.A. Manz are addressed through the
presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO$_3$ and
La$_2$Ce$_2$O$_7$, using our previously presented method for calculating
Hirshfeld-I charges in Solids [J. Comput. Chem.. doi: 10.1002/jcc.23088]. It is
shown that the use of pseudo-valence charges is sufficient to retrieve the full
all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present
timing results of different systems, containing up to over $200$ atoms,
underlining the relatively low cost for large systems. A number of theoretical
issues is formulated, pointing out mainly that care must be taken when deriving
new atoms in molecules methods based on "expectations" for atomic charges.Comment: 7 pages, 2 Tables, 2 figure
Calculation of Wave-functions with Frozen Orbitals in\ud
Mixed Quantum Mechanics/Molecular Mechanics\ud
methods. II. Application of the Local Basis Equation.

The application of the local basis equation1 in mixed quantum mechanics/molecular\ud
mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) meth-\ud
ods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals\ud
that minimize the energy of the system and it exhibits good convergence properties\ud
in a self-consistent field solution. These features make the equation appropriate to\ud
be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of\ud
frozen localized orbitals connecting the subsystems. Calculations performed for several\ud
properties in divers systems show that the method is robust with various choices of the\ud
frozen orbitals and frontier atom properties. With appropriate basis set assignment it\ud
gives results equivalent with those of a related approach2 using the Huzinaga equation.\ud
Thus the local basis equation can be used in mixed QM/MM methods with small size\ud
quantum subsystems to calculate properties in good agreement with reference Hartree-\ud
Fock-Roothaan results. It is shown that bond charges are not necessary when the\ud
local basis equation is applied, although they are required for the self-consistent field\ud
solution of the Huzinaga equation based method. On the other hand, the deformation\ud
of the wave-function near to the boundary is observed without bond charges and this\ud
has a significant effect on deprotonation energies but a less pronounced effect when the\ud
total charge of the system is conserved. The local basis equation can also be used to\ud
define a two layer quantum system with nonorthogonal localized orbitals surrounding\ud
the central delocalized quantum subsystem
Calculation of Wave-functions with Frozen Orbitals in\ud
Mixed Quantum Mechanics/Molecular Mechanics\ud
methods. I. Application of the Huzinaga Equation.

Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechan-\ud
ics/molecular mechanics (QM/MM) methods make computations feasible for extended\ud
chemical systems by separating them into subsystems that are treated at different level\ud
of sophistication. In many applications the subsystems are covalently bound and the\ud
use of frozen localized orbitals at the boundary is a possible way to separate the sub-\ud
systems and to ensure a sensible description of the electronic structure near to the\ud
boundary. A complication in these methods is that orthogonality between optimized\ud
and frozen orbitals has to be warranted and this is usually achieved by an explicit or-\ud
thogonalization of the basis set to the frozen orbitals. An alternative to this approach is\ud
proposed by calculating the wave-function from the Huzinaga-equation that guaranties\ud
orthogonality to the frozen orbitals without basis set orthogonalization. The theoreti-\ud
cal background and the practical aspects of the application of the Huzinaga equation\ud
in mixed methods is discussed. Forces have been derived to perform geometry opti-\ud
mization with wave-functions from the Huzinaga-equation. Various properties have\ud
been calculated applying the Huzinaga-equation for the central QM subsystem, repre-\ud
senting the environment by point charges and using frozen strictly localized orbitals\ud
to connect the subsystems. It is shown that a 2-3 bond separation of the chemical\ud
or physical event from the frozen bonds allows a very good reproduction (typically\ud
around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme\ud
provides an appropriate framework for mixed QM/QM and QM/MM methods
Monte Carlo configuration interaction applied to multipole moments,
  ionisation energies and electron affinities

The method of Monte Carlo configuration interaction (MCCI) [1,2] is applied
to the calculation of multipole moments. We look at the ground and excited
state dipole moments in carbon monoxide. We then consider the dipole of NO, the
quadrupole of the nitrogen molecule and of BH. An octupole of methane is also
calculated. We consider experimental geometries and also stretched bonds. We
show that these non-variational quantities may be found to relatively good
accuracy when compared with FCI results, yet using only a small fraction of the
full configuration interaction space. MCCI results in the aug-cc-pVDZ basis are
seen to generally have reasonably good agreement with experiment. We also
investigate the performance of MCCI when applied to ionisation energies and
electron affinities of atoms in an aug-cc-pVQZ basis. We compare the MCCI
results with full configuration-interaction quantum Monte Carlo [3,4] and
`exact' non-relativistic results [3,4]. We show that MCCI could be a useful
alternative for the calculation of atomic ionisation energies however electron
affinities appear much more challenging for MCCI. Due to the small magnitude of
the electron affinities their percentage errors can be high, but with regards
to absolute errors MCCI performs similarly for ionisation energies and electron
affinities.Comment: 12 pages, 20 figure