46 research outputs found
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials
Machine learning plays an important and growing role in molecular simulation.
The newest version of the OpenMM molecular dynamics toolkit introduces new
features to support the use of machine learning potentials. Arbitrary PyTorch
models can be added to a simulation and used to compute forces and energy. A
higher-level interface allows users to easily model their molecules of interest
with general purpose, pretrained potential functions. A collection of optimized
CUDA kernels and custom PyTorch operations greatly improves the speed of
simulations. We demonstrate these features on simulations of cyclin-dependent
kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water.
Taken together, these features make it practical to use machine learning to
improve the accuracy of simulations at only a modest increase in cost.Comment: 16 pages, 5 figure
OpenMM 8:Molecular Dynamics Simulation with Machine Learning Potentials
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features in simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations with only a modest increase in cost.</p
Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions
In order to carry out a detailed
analysis of the molecular static polarizability, which is the response
of the molecule to a uniform external electric field, the molecular
polarizability was computed using the finite-difference method for
21 small molecules, using density functional theory. Within nine charge
population schemes (Löwdin, Mulliken, Becke, Hirshfeld, CM5,
Hirshfeld-I, NPA, CHELPG, MK-ESP) in common use, the charge fluctuation
contribution is found to dominate the molecular polarizability, with
its ratio ranging from 59.9% with the Hirshfeld or CM5 scheme to 96.2%
with the Mulliken scheme. The Hirshfeld-I scheme is also used to compute
the other contribution to the molecular polarizability coming from
the induced atomic dipoles, and the atomic polarizabilities in eight
small molecules and water pentamer are found to be highly anisotropic
for most atoms. Overall, the results suggest that (a) more emphasis
probably should be placed on the charge fluctuation terms in future
polarizable force field development and (b) an anisotropic polarizability
might be more suitable than an isotropic one in polarizable force
fields based entirely or partially on the induced atomic dipoles
PSI4 1.4 : Open-source software for high-throughput quantum chemistry
PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.Peer reviewe
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features automatically work on all supported hardware types (including both CPUs and GPUs) and perform well on all of them. In many cases they require minimal coding, just a mathematical description of the desired function. They also require no modification to OpenMM itself and can be distributed independently of OpenMM. This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community
Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development
Psi4NumPy demonstrates the use of efficient computational kernels from the open-
source Psi4 program through the popular NumPy library for linear algebra in Python
to facilitate the rapid development of clear, understandable Python computer code for
new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods,
including self-consistent field (SCF), SCF response, many-body perturbation theory,
coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation
theory. Further, several reference codes have been integrated into Jupyter notebooks,
allowing background and explanatory information to be associated with the imple-
mentation. Psi4NumPy tools and associated reference implementations can lower the
barrier for future development of quantum chemistry methods. These implementa-
tions also demonstrate the power of the hybrid C++/Python programming approach
employed by the Psi4 program.
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