CCP5: The computer Simulation of Condensed Phases.

Lead Research Organisation: University of Bath
Department Name: Chemistry

Abstract

CCP5 provides support for all UK scientists engaged in developing and exploiting computer simulation methods for condensed matter systems. It supplies the main forum for atomistic simulation studies in the UK, is committed to developing new codes and techniques and fosters the application of simulation methods to an increasingly diverse range of scientific areas in both academia and industry. A distinctive feature of CCP5 is its successful strategy of developing and disseminating new codes and methods across all classes of materials, which means that many scientific areas have benefitted from CCP5 involvement. These include, but are not limited to, solid state materials, polymers, micelles, liquids, liquid mixtures, liquid crystals, surfaces and interfaces, homogeneous and heterogeneous catalysts, minerals and biosystems. Furthermore, by focussing on many different techniques the community can transfer knowledge and expertise across a wide range of disciplines. The primary tools that are used and supported are classical molecular dynamics, Monte Carlo and energy minimisation methods covering atomistic through to multi-molecular systems. UK modelling is at the fore-front of international research, but continued support for new code and technique development in this area is essential, if the UK is to address the major international challenges of pushing atomistic modelling to much longer time- and length-scales, linking first principles (quantum) and innovative coarse-grained and mesoscale methods to provide accurate multi-scale methods.

Planned Impact

Support of CCP5 will provide benefit for a large number of researchers in academia and industry in the UK, who use molecular simulation methods in the course of their work. Currently, there are 373 UK members, although with nearly 6000 software license registrations the benefit of the software is felt by a far larger community. By extension of the vibrant molecular simulation community within the UK, world science also benefits from the progress, innovation, cultural exchange and software that the project engenders. Furthermore, by continuing the training and development of the usability of simulation codes for the non-specialists, this group of users is expected to grow.

The research and development groups in UK industry also benefit as computer simulation is often seen as a viable alternative to costly experimental screening and test-bedding. In addition, many companies have good links with academic groups working in this area who will also be able to deliver new ideas and fundamental understanding of a range of materials of commercial value to UK industry, which coupled with the underpinning science will assist in the development of innovative future technologies. Industry will also benefit from the trained personnel coming from the different research groups that make use of the software and training supplied by CCP5. In addition, CCP5 members from industry regularly attend workshops to which international speakers have been invited. This enables industry to keep abreast of the cutting-edge challenges that face the computer simulation community.

The societal benefits will primarily be made through the subsequent development of new materials that will be cheaper and more environmentally friendly and biocompatible; thereby improving the well-being of those employed in the relevant industries as well as the general populations who are affected by the environmental and medical impacts of the current generation of materials.

Publications

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Archer A (2014) Order parameter and connectivity topology analysis of crystalline ceramics for nuclear waste immobilization. in Journal of physics. Condensed matter : an Institute of Physics journal

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Cox SJ (2012) Non-hexagonal ice at hexagonal surfaces: the role of lattice mismatch. in Physical chemistry chemical physics : PCCP

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Crabtree J (2013) Simulation of the Adsorption and Transport of CO 2 on Faujasite Surfaces in The Journal of Physical Chemistry C

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Davidchack RL (2015) New Langevin and gradient thermostats for rigid body dynamics. in The Journal of chemical physics

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Dutta G (2012) Activation of carbon dioxide over zinc oxide by localised electrons. in Chemphyschem : a European journal of chemical physics and physical chemistry

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Gray A (2012) Mapping application performance to HPC architecture in Computer Physics Communications

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Katsoulidis AP (2014) Guest-adaptable and water-stable peptide-based porous materials by imidazolate side chain control. in Angewandte Chemie (International ed. in English)

 
Description This grant funds the network, CCP5, which provides support for all UK scientists engaged in developing and exploiting computer simulation methods for condensed phase systems. CCP5 currently has 458 UK members; these include research active academic faculty staff in 34 different UK Universities as well as at least 17 other UK industrial, charitable or government organisations, excluding STFC. In many of the universities, the CCP5 member is the lone exponent of his/her field in that University, and so the CCP5 network activities are crucial in enabling these academics to be part of a critical mass. In accomplishing this, CCP5 has focussed on two major classes of activity: developing the academic community of condensed phase modellers in the UK, and then developing software for this community to use. A distinctive feature of CCP5 is its successful strategy of developing and disseminating new codes and methods across all classes of materials, which means that many scientific areas have benefitted from CCP5 involvement. These include solid state materials, polymers, micelles, liquids, liquid mixtures, liquid crystals, surfaces and interfaces, homogeneous and heterogeneous catalysts, minerals and biosystems. Furthermore, by not limiting the application area, both in terms of the techniques and the network activities, the community can readily transfer knowledge and expertise across a wide range of disciplines. The primary tools that are used and supported continue to be classical molecular dynamics, Monte Carlo and energy minimisation methods covering atomistic through to multi-molecular systems. However, to address the major scientific challenges increasing effort is being applied to pushing atomistic modelling to much longer time- and length-scales, and linking with first principles (quantum), coarse-grained and mesoscale methods to provide accurate multi-scale methods.
The other essential and continued requirements are for training, nurturing collaborations, disseminating new techniques, and fostering new solutions to fundamental problems. This is especially important for "early career researchers" and PhD students working on condensed phases. A leading example of the commitment to training is the world renowned CCP5 Summer School, which is the flagship international training school in molecular simulation in which leading members of the community freely give their time. In addition, the programme of workshops, international visitors, and Annual Meetings provide the opportunities for collaborations and developing new techniques and skills.

This research supports the development of the following simulation codes: i. DL_POLY (I Todorov) is a general purpose molecular dynamics (MD) package and is a major tool for the CCP5 community. ii. DL_MONTE (JA Purton) is a new general purpose Monte Carlo (MC) package iii. DL_MESO (M Seaton) provides mesoscale functionality and includes the 2 main techniques: Dissipative particle dynamics (DPD) and Lattice Boltzmann equation (LBE), iv. DL_FIELD (CW Yong) is a software tool to facilitate use of other codes particularly for biological systems, v. ChemShell (TW Keal) is for bridging quantum (QM) and molecular modelling (MM).
Exploitation Route The Network provides: i. Research Software, which enables both academic and industrial researchers to tackle new simulation based research projects. ii. Connecting the Community, allowing researchers to share and develop ideas, iii. Training the Next Generation, by providing summer school and training workshops,.
Sectors Aerospace, Defence and Marine,Chemicals,Electronics,Energy,Environment,Manufacturing, including Industrial Biotechology

URL http://www.ccp5.ac.uk/
 
Description There are a wide range of activities undertaken by those who benefit from CCP5 software and training. There have been a number of case studies, which illustrate the impact. Two of these are included here for brevity. The first includes work by R Strange, Liverpool and C Yong, STFC on Cytosolic Cu, Zn superoxide dismutase (SOD1), which is a critical component of the cellular defence against reactive oxygen species, Mutant forms of Cu-Zn superoxide dismutase (SOD1) have been directly linked to 20% of cases of familial amyotrophic lateral sclerosis (ALS; aka 'motor neuron disease') a fatal, progressive neurodegenerative condition with no known cure as well as several other neurodegenerative diseases and is reported to be a probable target for oxidative damage in Alzheimer's (AD) and Parkinson's diseases and in Down Syndrome. New data and insights include; protection against self-aggregation of SOD1 molecules can be partially restored by incorporating a single Zn molecule per dimer, and the identity of the segment of the enzyme structure that forms the 'core seed' for aggregation of pathogenic A4V in dimeric SOD1. They are also able to link this result to our parallel studies in fragment based medicinal chemistry, which are aimed at stabilising the mutant dimer (a manuscript is being prepared). A second case study, involves a consortium consisting of STFC, Unilever, Syngenta, Infineum and Novidec have been exploring the potential of CAF, using mesoscale simulation, to accelerate the design and optimisations of new liquid formulations in a variety of industry sectors. Of key importance to the success and future of this work has been the DL_MESO simulation package, in particular the DPD code. The DL_MESO_DPD code, developed as a CCP5 flagship project, is the main simulation engine of the CAF project, and was selected due to its world leading functionality and performance. New knowledge has been developed concerning the application of the DPD method to liquid product formulation in an industrial research and development pilot study; in particular the appropriate methodology has been identified. The applicability of the method has been demonstrated for a number of industry use cases from laundry detergent to oil additive optimisation. Deficiencies within the existing models have been identified and methods to overcome these deficiencies have been proposed.
Sector Aerospace, Defence and Marine,Chemicals,Education,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology
Impact Types Societal,Economic

 
Description Software Infrastructure Call
Amount £548,153 (GBP)
Funding ID EP/P022308/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 02/2020
 
Title DL_CGMAP, VOTCA, extended functionality and workflows in DL_POLY for coarse-grain simulation 
Description The DL_CGMAP utility allows to create a coarse-grain representation of a molecular full-atom system to be modelled by using DL_POLY-2 or DL_POLY-4 software. In addition to DL_CGMAP, a fully-featured workflow interface between DL_POLY and (internationally developed) VOTCA package allows to optimise state-of-the-art CG models with the use of DL_POLY-2 or DL_POLY-4 simulation engines. Also associated with this (CG) software development effort is a set of routines within DL_POLY-4 that enable analyses of intra-molecular interactions and creation of the corresponding numerical (tabulated) inputs for CG models involving bonded interactions based on the relevant potentials of mean force. 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact The developed tools have enabled CG methodologies to the academic users of DL_POLY, e.g. the group of Prof. Mark Wilson, University of Durham; the group of Dr. Paola Carbone, University of Manchester. The dissemination of the outcomes is carried out in the form of lectures and tutorials at the biannual DL_Software workshop. 
URL http://www.ccp5.ac.uk/projects/ccp5_cg
 
Description Collaboration on coarse-grain methods with international VOTCA team 
Organisation Los Alamos National Laboratory
Country United States 
Sector Public 
PI Contribution Extending the functionality in DL_POLY for coarse-grain simulation. Creating a coarse-graining helper utility DL_CGMAP, and an interface between DL_POLY and the internationally developed CG software VOTCA.
Collaborator Contribution In-kind contribution due to the international team effort (coordinated from the Los Alamos National Laboratory) to create and support an interface between DL_POLY and VOTCA.
Impact A. V. Brukhno, Density Transferability via Coarse Graining of Two Molecules: The Case of Lipids (DOPC), 2-nd CCPBioSim/CCP5 Multiscale Modelling Conference, University of Manchester, 13-15 April 2016.
Start Year 2013
 
Title A simulation workflow interface: VOTCA - DL_POLY, within the VOTCA package 
Description The interface allows for the (internationally developed) VOTCA package for systematic coarse-graining to be used in conjunction with DL_POLY simulation engines (both versions: 2 and 4) for optimisation of CG models based on the more detailed atomistic (full-atom) representarion of a molecular system. 
Type Of Technology Software 
Year Produced 2014 
Open Source License? Yes  
Impact Creation of the interface enabled a new type of model optimisation, based on a few novel methodologies available in VOTCA, and also new type of (CG) simulations with the use of DL_POLY packages. The developed workflow tools have enabled CG methodologies to the academic users of DL_POLY, e.g. the group of Prof. Mark Wilson, University of Durham; the group of Dr. Paola Carbone, University of Manchester. The dissemination of the outcomes is carried out at the biannual DL_Software workshops in the form of presentations and tutorials. 
URL http://www.ccp5.ac.uk/projects/ccp5_cg
 
Title Analyses and tabulated input routines for bonded interactions within the DL_POLY-4 package 
Description A few special routines within the DL_POLY-4 software for performing analyses of the probability distributions of intra-molecular (bonded) interactions, and also creation of the numerical (tabulated) inputs for these interactions (via potential of mean force). Altogether, the routines extend the functionality in DL_POLY-4 to MD simulation of coarse-grain systems. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact A new type of analyses and simulations has been enabled within DL_POLY-4 package, widening the range of its application to coarse-grain (CG) condensed/soft matter systems. The developed tools have enabled CG methodologies to the academic users of DL_POLY, e.g. the group of Prof. Mark Wilson, University of Durham; the group of Dr. Paola Carbone, University of Manchester. The dissemination of the outcomes is carried out at the biannual DL_Software workshops in the form of presentations and tutorials. 
URL http://www.ccp5.ac.uk/projects/ccp5_cg
 
Title Coarse Grain Modelling 
Description The software was designed to provide new software tools to allow those interested in modelling soft matter 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 and hence require using a coarse grain (CG) approach. 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 (www.votca.org) 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. 2. A stand-alone tool for CG mapping - DL_CGMAP. 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. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact The software has only recently been developed and is still be actively tested. 
URL http://www.ccp5.ac.uk/projects/ccp5_cg.shtml
 
Title DL_CGMAP: a tool to create and analyse coarse-grain models based on atomistic DL_POLY simulation 
Description A model coarse-graining helper utility DL_CGMAP (partly based on utils from DL_POLY CLASSIC distribution). 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact The DL_CGMAP utility allows for mapping of the atomistic (aka full-atom) DL_POLY (both Classic and Vanilla) models and simulation trajectories onto a less detailed, i.e. coarse-grain, representation. As such, it enables for new type, coarse-grain (CG) simulations to be prepared, carried out and analysed with the use of DL_POLY package(s). The dissemination of the outcomes is carried out at the biannual DL_Software workshops in the form of presentations and tutorials. 
URL http://www.ccp5.ac.uk/projects/ccp5_cg
 
Description CCP5 Sponsored Industry Day (joint with the RSC) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Joint Industry Day with invited speakers from a wide range of industries
Year(s) Of Engagement Activity 2016
 
Description DL_Software workshops, biannual 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Biannual DL_Software workshop(s) are aimed at postgraduate students and professional researchers (from both academia and industry) who are either using or intend to use in the future the CCP5 supported software packages and tools, such as DL_POLY, DL_MESO, DL_MONTE, DL_FIELD, DL_CGMAP etc. My contribution to these workshops has been twofold: (i) presentation of two flagship projects and the associated software, DL_CGMAP (2014 - 2017) and DL_MONTE-2 (2015 - 2018); (ii) practical tutorials in the usage of the respective software for the workshop attendees. The purpose was to raise the (potential) users' awareness about the CCP5/DL software as well as provide training to the national and international students and active researchers.
Year(s) Of Engagement Activity 2014,2015,2016,2017,2018
URL https://www.ccp5.ac.uk/software
 
Description Non-equilibrium Simulation School (NESS) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Summer School
Year(s) Of Engagement Activity 2015
 
Description Outreach Talk At School (Argentina) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact School visit in Patagonia, Argentina and short talk.
Year(s) Of Engagement Activity 2016
 
Description School Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Outreach Talk at School, which sparked questions and discussion afterwards.
Year(s) Of Engagement Activity 2016
 
Description School Visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Talk at English-speaking school in Argentina, school reported increased interest in area, and many questions following the talk and question session.
Year(s) Of Engagement Activity 2016
 
Description Schools Talk (Bristol) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk to 6th form school students and teachers - sparked questions and discussion afterwards.
Year(s) Of Engagement Activity 2017
 
Description Sponsored visit by Ignacio Pagonabarraga (University of Barcelona) - Series of lectures and discussions. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sponsored lecture tour by Ignacio Pagonabarraga (University of Barcelona)
Year(s) Of Engagement Activity 2016
 
Description Sponsored visit by Mark Tuckerman (New York University) - Series of Talks and Discussions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sponsored visit to the UK (several universities visited by Prof. Tuckerman)
Year(s) Of Engagement Activity 2017
 
Description Sponsored workship - Reactive force fields, from development to applications 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Sponsored workshop for training in this emerging area
Year(s) Of Engagement Activity 2015
 
Description Sponsored workshop - Advances in Li-battery research (Loughborough) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sponsored workshop in this key area
Year(s) Of Engagement Activity 2015
 
Description Sponsored workshop - DPD training 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training in this important emerging field.
Year(s) Of Engagement Activity 2015
 
Description Talk at Catedra Europa, Universidad del Norte, Barranquilla, Colombia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited plenary lecture (in Spanish) including a discussion of radiation damage simulations and CCP5.
Year(s) Of Engagement Activity 2016