CCP5 Flagship project - CG mapping tools

CCP5 Flagship Project: Coarse Grain Modelling

An important challenge, particularly faced by the soft matter community, is to understand and predict the phase behaviour and stability for systems where the numbers of atoms required are too large for atomistic MD and/or suffer from the time constraints of observing slowly evolving processes. One method to overcome this for complicated molecular structures such as polymers, liquid crystals and biomolecules is to reduce the number of degrees of freedom by using coarse grained (CG) models in which several atoms are grouped into effective interaction sites (CG sites or "beads"). Thereby a vast amount of 'uninteresting' local scale patterns of motion (with relatively short relaxation times), can be excluded from consideration. This makes simulation of a CG system significantly less resource and time demanding. For this reason, during the last decade multiscale CG simulations have gained increasingly important role in the studies of long time/scale phenomena that are still inaccessible in traditional "brute-force" atomistic simulations.

The objective of the new flagship project is to introduce this functionality within the DL_POLY simulation package, allowing UK groups to leverage their existing expertise with this software to reach longer time and length scales.The idea is to bring in a true 'on-the-fly' multiscale modelling capabilities to the UK academic community, where the codes will automatically generate force-fields and potential models applicable at different length and time scales.

This project will allow a wide-range of novel simulation approaches aimed at tackling the exsiting fundamental and practical problems in such quickly advancing areas as (bio)molecular sensors, catalysis (reactions and substrate/catalyst interactions), materials design and pharmaceutical formulation (heterostructures; nano-devices; drug-delivery systems), energy materials (electrolyte/electrode interfaces in batteries and fuel cells) biomimetic materials; and this list is not exhaustive.

Progress so far: tools for coarse-graining of atomistic systems

Along the agenda described above, systematic coarse-graining tools, to be used in conjunction with the available DL_POLY package(s), are being developed by Dr.AndreyBrukhno (The University of Bath, in collaboration with the DL_POLY development team, Daresbury Laboratory and the molecular modelling group of Dr. Paola Carbone, The University of Manchester).

There are two aspects to the CG approach that has been undertaken:

1. A fully featured interface has been introduced between DL_POLY and VOTCA, the latter being the well-known nowadays Versatile Object-oriented Toolkit for Coarse-graining Applications ( introduced in 2009 by the theoretical group Prof. Kurt Kremer [J. Chem. Theor. Comp. 2009, vol. 5(12), p. 3211] and now being further developed at UI-UC, University of Cambridge and LANL.

By now the latest version of DL_POLY (4.06+) can be used as MD simulation engine within the environment of VOTCA package (v1.3+). Thereby the systematic coarse-graining methodologies available in VOTCA have been enabled for DL_POLY users. The DL_POLY/VOTCA combination has been successfully tested on the study cases from the VOTCA tutorials, which are downloadable for familiarising and benchmarking purposes.

Both DL_POLY and VOTCA are well-suited for highly parallel computation (HPC) environments. For example, the tests were carried out on an HPC cluster Scarf. The implementation on Archer (former Hector) is being benchmarked.

Additional functionality related to the CG model preparation has also been implemented directly within the latest version of DL_POLY (4.06+), allowing for obtaining and using user-defined tabulated force-fields, including both bonded and non-bonded interactions (see DL_POLY manual).

2. A stand-alone tool for CG mapping - DL_CGMAP - is also being developed by Dr. Brukhno. This additional tool is aimed at providing the academic community using DL_POLY with a set of "in-house" utilities for coarse-graining and supplementary analysis of trajectories generated by DL_POLY.

At present, the pilot version of DL_CGMAP is available, enabling the following CG functionality for DL_POLY users (for details see its manual):

(i) Setting up a highly-customisable CG representation (or "mapping") of an atomistic system (previously simulated with the use of DL_POLY). The output includes the corresponding template CG force-field file (FIELD_CG, where bonded and angular interactions are to be specified by the user) and coarse-grained configuration and trajectory files (CONFIG_CG, REVCON_CG, HISTORY_CG) which can be directly used as input for a fresh DL_POLY run on the obtained CG system. Note that the main input file for DL_CGMAP assumes XML-format (CG_MAP.xml) which closely resembles the mapping format used by VOTCA.

(ii) In addition, it is possible to calculate pairwise radial distribution functions (RDF), g(rij), based on the obtained CG representation. The user has a choice of calculating either the overall (over the entire system), the inter- or intra-molecular distributions as well as a single distribution for a particular pair of CG "beads". Obviously, this way one can use DL_CGMAP tool for analysis of atomic group distributions, irrespective of any coarse-graining purpose whatsoever.

Left: An illustration of a coarse-grain model for a phospholipid molecule (DOPC) that produces a proper bilayer.
Right: The animation illustrates the example supplied with DL_CGMAP tool (see bench20* directories) - coarse-graining of a peptide 15-mer, one residue per CG bead (only for illustration purposes).

Future development will see integration of DL_CGMAP as an interface for multi-scale inter-conversion of system models within the CCP5 Software. For instance, a stand-alone DL_POLY CG mapping capability is to be integrated with DL_FIELD and DL_ANALYSER to encapsulate a complete CG software suite.

For more information about this project, please contact Dr.AndreyBrukhno: or (if faster response is required).


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