Driving torsion scans with wavefront propagation.

Yudong Qiu,Lee-Ping Wang,Hyesu Jang,Daniel G A Smith,Mudong Feng,Chaya D Stern

doi:10.1063/5.0009232

Abstract

The parameterization of torsional/dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. 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. 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. 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. In this paper, we propose a systematic and versatile workflow called 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. 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. The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.

Highlights

The potential energy surface along torsional dihedral angle degrees of freedom is a crucial part of model potentials for computer simulations of bio/organic molecules and polymers, including commonly used molecular mechanics force fields
In this paper we propose a systematic and versatile workflow called 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 Quantum mechanical (QM) data for force field development
Geometry optimizations were carried out in the TeraChem software package,[26,27] in which energies and gradients were calculated with density functional theory (DFT)

Summary

Introduction

The potential energy surface along torsional dihedral angle degrees of freedom is a crucial part of model potentials for computer simulations of bio/organic molecules and polymers, including commonly used molecular mechanics force fields. The four-body energy term for proper torsion in most force fields uses a periodic functional form of the dihedral angle φabcd represented as a truncated Fourier series, i.e. “1-4 interactions”), which may be modified from conventional non-bonded terms using scaling factors or alternative parameter values.[9] Because the 1-4 distance depends strongly (but not exclusively) on the torsion angle, it may be considered as another contribution to the torsional potential energy

Methods

Results

Conclusion