REGISTRATION – Version 4.11, released July 2024
______________________________________________
What’s new in Version 4.11
- Produce force field model files for Gromacs simulation package (gro, itp, top and mdp).
- Automatic single-point calculations in Gromacs (if supplied) after conversion.
- Inclusion of more organic solvents for setting up solution models (see solvent_list in the solvent/ folder)
- General force field libraries update.
________________________________________________
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.
Primary Functions
- Force field model convertor: Single-step conversion of user’s molecular configuration into FF model files for DL_POLY and Gromacs MD software packages 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, TraPPE-EH, PCFF, CVFF, COMPASS, Inorganic (oxides, clays, glass, zeolites), MISC_FF, etc.
Unique Capabilities
- 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.
![](https://www.ccp5.ac.uk/wp-content/uploads/2022/11/popc_ps-1.bmp)
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)
![](https://www.ccp5.ac.uk/wp-content/uploads/2022/11/polyMG-1024x952.jpg)
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).
![](https://www.ccp5.ac.uk/wp-content/uploads/2022/11/silk_fibrion-2.jpg)
Protein-based systems
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)
![](https://www.ccp5.ac.uk/wp-content/uploads/2022/11/graphene_cellulose-2.jpg)
Nano-composite materials
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)
![](https://www.ccp5.ac.uk/wp-content/uploads/2022/11/zsm5_methane.jpg)
Porous materials
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)
Relevant Links
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)
DL_F Notation:
- 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
DL_FIELD references
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)