Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<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>

scholarly journals Automated conformational energy fitting for force-field development

2008 ◽  
Vol 14 (8) ◽  
pp. 667-679 ◽  
Author(s):  
Olgun Guvench ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Conformational Energy ◽  
Field Development ◽  
Force Field Development

Molecular mechanics force-field development for amino acid zwitterions

2003 ◽  
Vol 24 (1) ◽  
pp. 111-128 ◽  
Author(s):  
K. N. Kirschner ◽  
A. H. Lewin ◽  
J. P. Bowen
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Molecular Mechanics ◽  
Field Development ◽  
Force Field Development

Force field development and simulations of senior dialkyl sulfoxides

2016 ◽  
Vol 18 (15) ◽  
pp. 10507-10515 ◽  
Author(s):  
Vitaly V. Chaban
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Ab Initio ◽  
Md Simulations ◽  
Field Development ◽  
Force Field Development ◽  
Structure And Dynamics ◽  
Ethyl Methyl ◽  
Methyl Sulfoxide ◽  
Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

Molecular modelling of (η6-arene)–Cr(CO)3 complex systems: force field development of the monosubstituted complexes

1999 ◽  
Vol 475 (2-3) ◽  
pp. 279-286 ◽  
Author(s):  
A. Elass ◽  
J. Mahieu ◽  
J. Brocard ◽  
G. Surpateanu ◽  
G. Vergoten
Keyword(s):  
Complex Systems ◽  
Force Field ◽  
Molecular Modelling ◽  
Field Development ◽  
Force Field Development
Sign in / Sign up

Export Citation Format

Share Document