REGISTRATION – Version 4.9, released November 2022
What’s new in Version 4.9
- COMPASS force field (public domain version)
- CHARMM36 force field for nucleic acids (CHARMM36_nucl)
- Conversion of Lennard-Jones 9-6 to 12-6 forms to make use of vdw mixing schemes for multiple potential systems.
- Allow solvation using solvent models from different force field schemes.
- Improvement on MISC_FF scheme: enable vdw mixing between different MOLECULE templates and inclusion of general Lennard-Jones of nm forms.
DL_FIELD is a utility software tool to setup force field (FF) models for molecular simulations such as the molecular dynamics (MD).
Software Development Strategy
To develop a user-friendly software tool that automatically process the complex molecular information with minimum user’s intervention and to speed up scientific outputs.
- Force field model convertor: Single-step conversion of user’s molecular configuration into FF model files for DL_POLY MD software based on user-selectable FF scheme.
- Force field editor: Edit or modify a standard FF scheme to produce customised schemes that is specific to a particular type of molecular model.
- Natural atom types descriptor: Automatic identification of chemical natural of every atom in the system.
- Available force fields: CHARMM, Amber, OPLS, PCFF, CVFF, COMPASS, Inorganic (oxides, clays, glass, zeolites), MISC_FF, etc.
- Universal atom typing (DL_F Notation). Include chemical metadata directly into simulations for results analysis.
- Integration of FF schemes into identical DL_FIELD format.
- Multiple FF model setup such as bio-inorganic models.
Selected Example models
Applicable to a wide range of models – proteins, nuclei acids, carbohydrates, drug molecules, complex networked structure, polymers, inorganic solids, minerals and the mixture thereof.
Complex organic systems
C. W. Yong, ‘Study of interactions between polymer nanoparticles and cell membranes at atomistic levels’ Phil. Trans. R. Soc. B 370, 20140036 (2015)
General organic and biomolecules
O.J. Hills, C.W. Yong, A.J. Scott, D.A. Devine, J. Smith, H.F. Chappell, ‘Atomic-scale interactions between quorum sensing autoinducer molecules and the mucoid P. aeruginosa exopolysaccharide matrix’ Sci. Rep. 12, 7724 (2022).
M.J. Haskew, B. Deacon, C.W. Yong, J.G. Hardy and S.T. Murphy, ‘Atomistic Simulation of water incorporation and mobility in bombyx mori silk fibrion’, ACS Omega 6, 35494-35504 (2021)
L. Kong, R. Alqus, C.W. Yong, I.T. Todorov, S.J. Eichhorn, R.A. Bryce, ‘Cellulose I-beta microfibril interaction with pristine graphene in water: Effects of amphiphilicity by molecular simulations’, J. Mole. Graphics Model. 118, 108336 (2023)
A.P. Hawkins, A. Zachariou, I.P. Silverwoord, et. al. ‘Combining quasielastic neutron scattering and molecular dynamics to study methane motions in ZSM-5’, J. Chem. Phys. 157, 184702 (2022)
DL_POLY particle-based dyanamics simulation software
DL_FIELD additional information, at DL_Software Digital Guide (DL_SDG)
DL_FIELD Tutorial – available at DL_Software Digital Guide (DL_SDG)
- Journal reference: C.W. Yong, ‘Description and implementations of DL_F Notation: A natural chemical expression system of atom types for molecular simulations’, J. Chem. Inf. Model. 56, 1405-1409 (2016)
- Additional information, available at SSRN: http://dx.doi.org/10.2139/ssrn.4254942
If you use DL_FIELD in your work, please quote the following reference:
C.W. Yong, ‘Description and implementations of DL_F Notation: A natural chemical expression system of atom types for molecular simulations’, J. Chem. Inf. Model. 56, 1405-1409 (2016)