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
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.
Publications
Womack JC
(2016)
Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package.
in The Journal of chemical physics
Vitale V
(2017)
Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.
in The Journal of chemical physics
Vitale V
(2015)
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in O NETEP
in Journal of Chemical Theory and Computation
Sutton EJ
(2018)
Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering.
in Biophysical journal
R.T. Bradshaw
(2016)
Electric fields in biomolecular systems using the AMOEBA polarizable force field
R.T. Bradshaw
(2016)
What has polarization ever done for us?
Mohamed NA
(2016)
Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.
in Journal of computational chemistry
Mardirossian N
(2017)
Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals.
in The journal of physical chemistry letters
Mao Y
(2017)
Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis.
in Journal of chemical theory and computation
Mao Y
(2016)
Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation.
in The Journal of chemical physics
Huggins D
(2018)
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
in WIREs Computational Molecular Science
Howard JC
(2017)
Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory.
in Journal of chemical theory and computation
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
Dziedzic J
(2019)
Mutually polarizable QM/MM model with in situ optimized localized basis functions.
in The Journal of chemical physics
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
Bradshaw RT
(2020)
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
in Journal of chemical information and modeling
Bradshaw RT
(2016)
Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.
in Journal of chemical theory and computation
Boschetto G
(2017)
Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
in The Journal of Physical Chemistry C
Albaugh A
(2016)
Advanced Potential Energy Surfaces for Molecular Simulation.
in The journal of physical chemistry. B
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/ |