Driving Torsion Scans with Wavefront Propagation

Abstract

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

“…different results when the same point is scanned from different direction), and to optimizations being trapped in local minima rather than the lowest energy structure at the grid point. As shown previously [40], these problems can be particularly severe for alkene motors, likely due to nontrivial size (48 atoms for Motor S) and high rotation barriers, but problems are largely alleviated by the TorsionDrive method. Energies and gradients were computed by the Psi4 package [41] for use in TorsionDrive.…”

“…We used the wavefront propagation algorithm implemented in TorsionDrive [40], an open source package, to generated QM surfaces of motors S, N and O ( Figure 1). TorsionDrive runs geometry optimizations constrained at each grid point multiple times, from different propagating directions, to find the lowest energy structure at that point.…”

The MolSSI QCArchive project: An open‐source platform to compute, organize, and share quantum chemistry data

“…QCF ractal can also run workflow “services” to orchestrate sophisticated computational campaigns built out of interdependent tasks. For example, a TorsionDrive 59 service will compute the energy surface of a molecule at a frozen set of dihedral coordinates. The TorsionDrive program is a standalone open‐source package 60 that implements an iterative procedure for computing smooth dihedral scans.…”

Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations

“…13,16,50,51 Lennard-Jones parameters were derived by QUBEKit from the atomic volumes using the Tkatchenko-Scheffler method. 15,17 Torsion parameter fitting on core fragments of the ligand sets followed the general methods used in previous studies, 13,22 though here we employ an interface between QUBEKit and the TorsionDrive package, 52 which improves the quality of both QM and MM torsion scans through its recursive wavefront propagation algorithm. Final force fields were output in xml format.…”