Potential Energy Surfaces of Various Accuracy for Bio-molecular Simulations
Lead Research Organisation:
Science and Technology Facilities Council
Department Name: Computational Science & Engineering
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
People |
ORCID iD |
| Ilian Todorov (Principal Investigator) |
Publications
Albaugh A
(2016)
Advanced Potential Energy Surfaces for Molecular Simulation.
in The journal of physical chemistry. B
Boateng HA
(2015)
Arbitrary order permanent Cartesian multipolar electrostatic interactions.
in The Journal of chemical physics
| Description | On the software side the project was overambitious. The length of funding, 2 years, and the effort for supervision (6%) were seriously underestimated for sustainable software implementation. |
| Exploitation Route | A viable plan for the suggested work, delivering methodological development (application maths), formulating solutions, prototyping, integration and testing (software development) in sustainable manner (continual testing and integration cycle) would have taken 3 to 4 years of length with 20-25% supervision effort. |
| Sectors | Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology |
| Description | 3rd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3), 28-29 September 2015, Boulder, Colorado, USA |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | http://wssspe.researchcomputing.org.uk/ |
| URL | http://wssspe.researchcomputing.org.uk/ |
| Description | First EU LEIT meeting, 27 February 2014, Brussels, Belgium |
| Geographic Reach | Europe |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://emmc.info/ |
| Description | First RSE Conference - 15-16 September 2016 @ Manchester |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | I was elected at the first voted for UK RSE Executive Committee to advise on its own future and work towards the recognition and professionalisation of software development work within research environments; as UK and USA academia and other research institutions, as well as advise and influence EPSRC and NSFon these needs, the path to and implications when addressing them. |
| URL | https://ukrse.github.io/conf2016 |
| Description | NSF-SI2 Software Institute Conceptualization for Molecular Simulation, 19-20 September 2014, Berkeley University, California, USA. |
| Geographic Reach | North America |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | NSF-SI2 Software Institute Conceptualization for Molecular Simulation. As a software owner, practitioner and visionary I was invited to provide opinion on amending and creating policies to preserve software outcomes in academia by ensuring, recognition, reward and advancement of research software engineers within the academic eco-system. |
| Description | NSF-SI2 Software Institute Conceptualization for Molecular Simulation, Houston, USA, 22 January 2015 |
| Geographic Reach | North America |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | NSF-SI2 Software Institute Conceptualization for Molecular Simulation initiative |
| Description | Multipolar Electrostatics - Henry Boateng at Bates College |
| Organisation | Bates College |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The principal author of the general (Cartesian) multipolar electrostatics methodology is a visiting scientist at STFC. He has visited twice since the grant ended and has worked on improving the software implementation and solving numerical challenges (singularities) with respect to bridging the multipolar and Druder polarisation technologies. |
| Collaborator Contribution | He has visited twice since the grant ended and has worked on improving the software implementation and solving numerical challenges (singularities) with respect to bridging the multipolar and Druder polarisation technologies. |
| Impact | The outcome is software functionality, capability and quality. Multidisciplinary: Physics, Chemistry, Mathematics, Materials, Software. |
| Start Year | 2015 |
| Description | SPME Electrostatics modernisation |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This is part of the DL_POLY modernisation exercise and involves Ian Bush as the materials science EPSRC software fellow at Oxford University |
| Collaborator Contribution | SPME Electrostatics verification, modularisation and general modernisation. |
| Impact | SPME Electrostatics verification, modularisation and general modernisation. |
| Start Year | 2018 |
| Title | DL_POLY_4 - CHARMM Druder polarisation compatibility |
| Description | General Purpose Molecular Dynamics Program |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Provides usability for CHARMM like models for self-polarisable force fields. |
| URL | http://www.ccp5.ac.uk/DL_POLY/ |
| Title | DL_POLY_4 - Shell (Druder) polarisation handled on multipolar level |
| Description | General Purpose Molecular Dynamics Program |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | The "Shell (Druder) polarisation handled on multipolar level" provide access to inclusion of more physics by accounting for induced polarisation in various materials models. |
| URL | http://www.ccp5.ac.uk/DL_POLY/ |
| Description | "DL_POLY multipolar electrostatics methodology and results" (Invited Speaker), Beyond point charges: novel electrostatic developments in force fields, CECAM-HQ-EPFL, Lausanne, Switzerland, 4-7 April, 2016 |
| 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 | 92. "DL_POLY multipolar electrostatics methodology and results" (Invited Speaker), Beyond point charges: novel electrostatic developments in force fields, CECAM-HQ-EPFL, Lausanne, Switzerland, 4-7 April, 2016 |
| Year(s) Of Engagement Activity | 2016 |
| Description | "DL_POLY multipolar electrostatics" (Invited Speaker), Advanced Potential Energy Surfaces, Division of Physical Chemistry, 252 National ACS Meeting, Philadelphia, PA, 21-25 August 2016. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 95. "DL_POLY multipolar electrostatics" (Invited Speaker), Advanced Potential Energy Surfaces, Division of Physical Chemistry, 252 National ACS Meeting, Philadelphia, PA, 21-25 August 2016. |
| Year(s) Of Engagement Activity | 2016 |
| Description | "Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces" (Invited Speaker), June 14-18, 2015, Telluride Research Science Center, Telluride, Colorado, USA |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | N/A |
| Year(s) Of Engagement Activity | 2015 |
| Description | "Two Day DL_SOFTWARE Workshop", 21-23 October 2014, TNI, Cork, Ireland |
| 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 | DL_Software activity |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.ccp5.ac.uk/ |
| Description | DL_POLY CECAM Extended Software Development Workshop for Atomistic, Meso- and Multiscale Methods on HPC Systems, 6-7 Sep 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | DL_POLY CECAM Extended Software Development Workshop for Atomistic, Meso- and Multiscale Methods on HPC Systems. |
| Year(s) Of Engagement Activity | 2018 |
| Description | DL_POLY'S 25TH ANNIVERSARY SPECIAL MEETING- 3rd November 2017 @ Chicheley Hall |
| 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 | The event was organised to celebrate the DL_POLY project anniversary and its successes with former and current project contributors and stakeholders. Molecular Simulation Special Issue To celebrate the project anniversary we have organised a Molecular Simulation special issue "DL_POLY: Twenty five years of molecular dynamics evolution". The papers will be refereed and will focus on modelling, methodology or numerical/algorithm/software developments related to or carried out with the help of DL_POLY (or its spinoffs DL_MULTI, DL_MESO_DPD). We are looking for high standard unpublished research as well as new angle reflections and summaries of recently published research (with appropriate citations and acknowledgements to originally published work) Submission Site Information for authors The submission deadline is at the end of January 2018. PROGRAMME 3 November 2017 08.30-09.00 Registration with Tea/Coffee 09.00-09.05 Official opening (Ilian Todorov) Chair: Ilian Todorov 09.05-09.35 Prof. Martin Dove (QMUL) - Molecular dynamics simulations of carbon capture by porous hybrid materials 09.40-10.10 Dr. Patrice Bordat (University of Pau) - Solvation and free energy module implemented in DL_POLY: Study for a preferential CO2/CH4 adsorption in silica monoliths 10.15-10.35 Tea/Coffee Break Chair: Tim Forester 10.40-11.10 Prof. John Harding (University of Sheffield) - Understanding biomineralisation: what has DL_POLY ever done for us? 11.15-11.45 Dr. Simone Melchionna (ISC-CNR) - Proteins and multiscale biology: the long time legacy of DL_POLY 11.50-12.20 Prof. Richard Catlow (UCL/University of Cardiff) - Molecular dynamics in Catalytic systems 12.25-13.25 Lunch Chair: Maurice Leslie 13.30-14.00 Dr. Kostya Trachenko (QMUL) - Using DL_POLY to understand radiation damage effects and soft matter (glasses, liquids, supercritical fluids) 14.05-14.35 Dr. P.-L. Chau (Institut Pasteur) - General Anaestheics and Membrane Interactions 14.40-15.10 Dr. David Quigley (University of Warwick) - The Hackademic Approach to Simulations with DL_POLY 15.10-15.30 Tea/Coffee Break Chair: Neil Allan 15.35-16.05 Prof. Steve Parker (University of Bath) - Atomistic Simulations of Oxide and Mineral Interfaces 16.10-16.40 Prof. Martyn Guest (University of Cardiff) - DL_POLY - A Performance Overview; Analysing, Understanding and Exploiting available HPC Technology 16.45-17.25 Closing Remarks by Prof. William Smith - A Short History of DL_POLY |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.ccp5.ac.uk/events/dl_poly_25 |
| Description | HPC and Molecular Modeling and Simulation Outreach - 15 December 2017 @ Sandymoor School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | STFC and science communities presentation to enthuse local school students to uptake further studies, student placements and have a career in the STEAM area. |
| Year(s) Of Engagement Activity | 2017 |
| Description | International CoSeC Review panel, 16-18 October 2018 in London |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Review the past 11 years of outcomes and contributions to CCP and HEC funding into the work of my institution and in particular within DL_Software. |
| Year(s) Of Engagement Activity | 2018 |
| Description | SLA International Review - Technopolis Ltd inteview (25 July 2018), international panel interview (17 October 2018, London) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The SLA International review accounts for the progress of the CoSeC program complementing CCPs and HECs in the UK acadeima. |
| Year(s) Of Engagement Activity | 2018 |