SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces
Lead Research Organisation:
University of Southampton
Department Name: Sch of Chemistry
Abstract
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Publications
Albaugh A
(2016)
Advanced Potential Energy Surfaces for Molecular Simulation.
in The journal of physical chemistry. B
Boschetto G
(2017)
Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
in The Journal of Physical Chemistry C
Bradshaw RT
(2016)
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.
in Journal of chemical theory and computation
Bradshaw RT
(2020)
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
in Journal of chemical information and modeling
Cave-Ayland C
(2017)
A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies.
in Journal of chemical theory and computation
Dziedzic J
(2019)
Mutually polarizable QM/MM model with in situ optimized localized basis functions.
in The Journal of chemical physics
Dziedzic J
(2016)
TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field.
in The Journal of chemical physics
| Description | Through this award we have explored the accuracy of a popular polarisable force field widely used in the biomolecular simulation community. We have found that it is able to reproduce hydration and solvation free energies with an accuracy broadly consistent with conventional fixed-charge force fields, but at significantly greater cost. This is disappointing, but perhaps unsurprising given the time that has been spent in optimising conventional fixed-charge models. More interestingly, however, we have also shown that the AMOEBA polarisable force field is able to reproduce the electric fields in proteins with an accuracy comparable to density functional theory, but at a fraction of the cost. Thus if electrostatics are particularly important, the polarisable force field represents a significant improvement over fixed charge models. |
| Exploitation Route | These data support the use of polarisable force fields in modelling protein electrostatics. This will likely be relevant to workers seeking to understand enzyme structure and function |
| Sectors | Pharmaceuticals and Medical Biotechnology |
| Description | CRUK |
| Amount | £301,105 (GBP) |
| Funding ID | C55730/A23562 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2017 |
| End | 12/2019 |
| Description | Postgraduate funding from Malaysian government |
| Amount | £115,632 (GBP) |
| Organisation | Ministry of Education Malaysia |
| Sector | Public |
| Country | Malaysia |
| Start | 02/2014 |
| End | 02/2017 |
| Description | RS Newton Fellowship |
| Amount | £99,000 (GBP) |
| Funding ID | NF171278 |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 02/2020 |
| Description | SI2 - Berkeley |
| Organisation | University of California, Berkeley |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Collaborator Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Impact | Outputs thus far have been conference posters. The collaboration is not multidisciplinary. |
| Start Year | 2013 |
| Description | SI2 - Caltech |
| Organisation | California Institute of Technology |
| Department | Division of Geological and Planetary Sciences |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Collaborator Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Impact | Conference posters thus far. This is not a multidisciplinary collaboration. |
| Start Year | 2013 |
| Description | SI2 - NYU |
| Organisation | New York University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Collaborator Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Impact | Conference posters thus far. This is not a multi-disciplinary collaboration |
| Start Year | 2013 |
| Description | SI2 - WUSTL |
| Organisation | Washington University in St Louis |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Collaborator Contribution | The EPSRC grant under which this contribution is reported is a joint grant with the NSF. In this project we share data and collaborate on methodology development and optimisation. |
| Impact | Conference posters thus far. This collaboration is not multi-disciplinary. |
| Start Year | 2013 |
| Description | Training workshop on using TINKER with the AMOEBA force field |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | We arranged a one-day training workshop on using the AMOEBA force field in the context of the TINKER molecular dynamics software. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://sites.google.com/site/amoebaworkshop/ |