SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces

Lead Research Organisation: University of Edinburgh
Department Name: Edinburgh Parallel Computing Centre


Molecular dynamics simulations provide a powerful tool to study a wide range of chemical and biochemical systems. The simulations provide a movie of the atoms diffusing over time, from which important dynamic and thermodynamic properties may be calculated. The reliability of these simulations is, however, limited by the accuracy of the model used to describe how the atoms in the system interact with each other. Conventional force fields, in which fixed charges are used, represent a major factor limiting the successful application of computer simulations to a variety of grand challenge problems in computational chemistry, biochemistry and materials science. Polarizable empirical force fields, which offer a clear and systematic improvement by allowing atom-centred charges to change depending on their environment, have been recently developed by most major research groups in force field development to increase accuracy. These advanced potential energy surfaces are important for the future of grand challenge applications such as the design of environmentally friendly materials, chemical reactions and reactivity critical for chemical synthesis, and biological complexity such as protein-drug interactions.

However, there are obstacles to using advanced potential energy surfaces for these grand challenge chemistry problems: the computational cost of the models, limited dissemination to a broad range of community codes, and lagging quality software implementations on HPC architectures and newer GPU and multicore hardware. To address these issues, we have organized a UK and US consortium that represents a broad cross section of the computational chemistry software community involved in chemical and biochemical applications, force field development, electronic structure methods, molecular dynamics algorithms, and software engineering with computer science experts. In this project, state-of-the-art polarizable potential energy functions will be consistently implemented and tested in a number of the most widely used simulation codes. The latest software development practices will be used to ensure that the freely-available developed software meets the highest standards of robustness, maintainability, and usability. New methodologies to improve the computational performance of these models will also be implemented. An important aspect of our work is to combine these latest force field models with quantum mechanical methods, allowing the accurate modelling of chemical reactivity and excited states. Our international collaboration between US and UK universities and HPC centres will ensure that the investment made in molecular simulation software is successfully deployed on current and emergent hardware and will also realize a long term payoff in community availability and sustainability. This project will lead to a step-change in the use of advanced potential energy surfaces by delivering consistent and sustainable implementations of the latest science on a diverse range of readily available and widely utilised software platforms.

Planned Impact

The software platforms within which the developments will be carried out in this proposal, TINKER, Amber, DL_POLY, ONETEP, and Q-Chem, comprise a diverse and popular suite of chemical software programs used for the simulation of molecular properties in gas or condensed phases. The close collaboration of experts in force field and electronic structure codes proposed here will allow us to develop important new methods and to communicate effectively to the wider chemical, biological and materials research communities. We aim to bring about a step change in molecular simulations both in the accuracy and the time scales that can be achieved and hence enable the end users to perform simulations at a whole new level of realism.

Academic research groups will benefit by being able to access the latest technology in potential energy surface calculations, consistently implemented in a range of distinctive classical and quantum mechanical computational chemistry codes. Not only will this allow these groups to perform a wider range of more accurate calculations than before, but the free availability of the software developed here will facilitate wider engagement by the academic community in terms of implementing our approaches in yet more codes, together with enabling further method development and optimisation.

The industrial community will also benefit through being able to access these new methods. Accurate potential energy functions allow intermolecular interactions to be described more completely, a crucial aspect leading to improvements in rational material and molecular design. The opportunities arising from advanced potential energy functions will therefore have a clear commercial benefit, improving our economic competitiveness by delivering new and more efficient products (such as greener and more efficient batteries, satisfying our energy needs in an environmentally friendly way), and delivering products that will enhance our quality of life through improved health and longevity (new drugs, for example). An important aspect of our proposal is the implementation and testing of accurate potential energy methods in a diverse range of widely-used software programs using the latest software design and development protocols. This will ensure the appropriate level of trust and confidence needed for software to be used in a commercial environment.

Policy makers will benefit through the more accurate calculations of molecular properties that the developed software will allow. This is particularly important given the current drive to reduce animal testing, of which the European Union REACH regulations are perhaps the clearest example. Our developed software therefore has the potential to impact public policy and legislation.

Another class of beneficiaries of this project will be the manufacturers of cutting edge HPC platforms. One of the main aims of our work is to harness the power of the latest HPC technologies to tackle chemical grant challenges. Through our access to top of the range national supercomputers and their manufactures we will assist them to make capability HPC more accessible to chemical problems. Our consortium is large enough to leverage the HPC manufacturers to view chemical applications as important user-cases when designing the next generation supercomputers.

Finally, the training of scientists working within our groups will make a significant impact. All will receive rigorous training in computational science, numerical methods and parallel programming, within a collaborative environment characterised by an ethos that embraces best practice in software development. This grant will therefore help to fill the skills gap recently identified by several international reports by delivering highly trained individuals with combined skills in computational science and software development.


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Description This grant has resulting in an enhanced version of the TINKER code, a code used to simulate biological systems. This allows more accurate and larger simulations to be carried out.
Exploitation Route This has produced sustainable software in the field of advanced potential energy surfaces.
Sectors Digital/Communication/Information Technologies (including Software)

Description A software demonstration was developed for the Wee Archie supercomputer to explain to children how molecular dynamics simulations work. Wee Archie is a suitcase sized supercomputer that has been used to showcase the science carried out on supercomputers, particularly to school children. The demonstration uses a molecular dynamics simulation code and shows the challenge of simulating large complex molecules but with a child friendly problem. The mouse major unitary protein (MUP) - or mouse wee - simulation shows how the smell in mouse wee is released slowly.
First Year Of Impact 2016
Sector Education
Impact Types Societal

Title AMOEBA scripts 
Description Set of scripts for setting up, minimizing, and running AMOEBA simulations entirely with OpenMM 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact These scripts help users run AMOEBA simulations with OpenMM 
Title TINKER Software Enhancements 
Description ENhanced version of the TINKER software - a molecular dynamics code. This includes various serial and parallel optimisations 
Type Of Technology Software 
Year Produced 2016 
Impact The software is now available on the ARCHER service, the UK National Supercomputer and therefore accessible by many scientists. These can in turn make impact. Accessible via a git hub repository: 
Description Contribution to the ARCHER booth at the Big Bang Fair 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact As part of the ARCHER booth at the Big Bang Fair, the project developed a demo to highlight the importance and relevance of molecular dynamics for school children. The demo ran on Wee ARCHIE, a mini supercomputer of raspberry Pis. ARCHER is the UK National Supercomputer and the project has time allocated on this system. The Big Bang Fair occurs at the NEC in Birmingham and in 2015 had over 70,000 people through the door across 4 days.
Year(s) Of Engagement Activity 2016
Description Organised a workshop at SC15 on "Producing High Performance and Sustainable Software for Molecular Simulation" 
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 This was a workshop organised at SC15, the premier HPC conference in our field. The workshop was selected from a peer review process. The purpose was to bring together experts form within and outwith the project to discuss the challenges associated with molecular simulation software and define how this software will need to develop to meet the challenges of next generation HPC architecture.
Year(s) Of Engagement Activity 2015