Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post–Hartree–Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

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CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

Computer simulations are powerful tools in order to figure out the physical and chemical phenomena occurring in the prebiotic environments, shedding light on the processes that led to the emergence of life on Earth. Indeed, the state-of-the-art theoretical methods have been developed for predicting molecular properties of the isolated systems and for describing the intermolecular interactions and the reactivity in a wide range of environments and boundary conditions. Such studies strongly help to unravel the various molecular contributions to the intricate experimental outcomes, allowing a deeper understanding of the underlying phenomena. This contribution provides an overview of the theoretical studies of prebiotic systems, drawing attention to some application of specific computational tools.

Computer Simulations of Prebiotic Systems

In this contribution, some issues related to the interpretation, simulation and modelling of solvent effects on the absorption and emission spectra of organic dyes are presented and discussed. First, a brief analysis of the physical basis of solvent effects on the electronic transitions is reported, in order to introduce the most important phenomena and quantities tuning the so-called solvatochromic shifts. This is followed by a general discussion of the most common models employed for the interpretation, simulation and prediction of such effects. A general and effective multilayer scheme is analyzed in some detail, which has been developed in the past years and is known to provide—in most cases—quantitative predictions of the spectral features of solvated molecules. Afterwards, starting from this general model, some approximations are introduced, leading to simplified and cost effective analytical schemes. In order to sketch a more complete perspective of the models still used by spectroscopists, phenomenological methods are critically discussed. Finally, broadening of spectral lines by both symmetric (solvent relaxation) and possibly asymmetric (vibronic) contributions is shortly analysed. In all cases, the theoretical bases of the methods, as well as practical applications and test cases are given, in order to clarify the most interesting aspects of all the discussed models.

Computational Spectroscopy in Solution: Methods and Models for Investigating Complex Systems

Computational Tools for Structure, Spectroscopy and Thermochemistry

A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution.

https://pubs.acs.org/doi/pdf/10.1021/acsomega.2c01110

Ivan Carnimeo

Papers

Computer Simulations of Prebiotic Systems

Computational Spectroscopy in Solution: Methods and Models for Investigating Complex Systems

Computational Tools for Structure, Spectroscopy and Thermochemistry

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution