DL_F Notation - a chemical-sensitive, natural atom typing notation for molecular simulations and results analysis

18 Pages Posted: 8 Nov 2022

Date Written: October 21, 2022

Abstract

DL_F Notation is a standardised atom type notation that contains cheminformatics data for molecular simulations such as the molecular dynamics (MD). The Notation is the unique feature implemented in DL_FIELD, a utility software program that facilitates the setting up of molecular force field (FF) models for DL_POLY MD simulation software. The Notation can be used to produce a consistent atom typing that is expressed in a natural chemical sense for a range of organic FF schemes. This document describes the need for a consistent atom typing format and facilitates the ease of setting up the FF models. The universality characteristics of the Notation will be briefly discussed followed by several example structures, to illustrate how the Notation can be interpreted.

Keywords: atom typing, cheminformatics, molecular simulations, force fields, chemical notations

Suggested Citation

Yong, Chin, DL_F Notation - a chemical-sensitive, natural atom typing notation for molecular simulations and results analysis (October 21, 2022). Available at SSRN: https://ssrn.com/abstract=4254942 or http://dx.doi.org/10.2139/ssrn.4254942

Chin Yong (Contact Author)

STFC Daresbury Laboratory ( email )

Warrington, Cheshire WA4 4AD
United Kingdom

HOME PAGE: http://ccp5.ac.uk/software

Do you have a job opening that you would like to promote on SSRN?

Paper statistics

Downloads
33
Abstract Views
215
PlumX Metrics