APES: Advanced Potential Energy Surfaces

Note: this is archived text

Bringing together UK and US force field expertise to improve molecular modelling.

Potential energy functions, which chemists confusingly refer to as force fields, are crucial in computational chemistry, especially molecular mechanics and molecular modelling. Established force field models implemented in computational chemistry software mostly use non-polarisable fixed point charge approximations. This is done because they are computationally cheap and give reasonable results for equilibrium properties and for homogeneous systems. However they fall short in describing many-body effects, dynamical properties, heterogeneous systems and systems that are out of equilibrium. This represents a major factor limiting the successful application of computer simulations to a variety of grand challenge problems in computational chemistry, biochemistry and materials science.

The "APES" (pronounced "A-PES") for Advanced Potential Energy Surfaces project is an NSF-EPSRC funded US-UK collaboration that aims to incorporate novel potential energy surface models into a range of computational chemistry packages. EPCC's two main contributions are to parallelise some of the codes to take advantage of the large-scale compute resources offered by supercomputing clusters such as ARCHER in the UK and Titan in the US, and to improve the integration and uptake of advanced models in established chemistry codes. The outputs from this project should equip researchers with better tools to advance their understanding of the structure and function of molecules.

In this project, we are using polarisable empirical force fields. These force fields allow atom-centred charges to change depending on their environment. They offer clear and systematic improvement in accuracy and are important for future grand challenge applications such as design of environmentally friendly materials, chemical reactions and reactivity, and biological complexity such as protein-drug interactions.

AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), is a prominent empirical polarisable force field developed by J. Ponder et al. and includes polarisable atomic multipoles through quadrupole moments derived directly from ab initio QM electron densities for small molecules and molecular fragments, allowing:

  • Replication of molecular polarisabilities and electrostatic potentials
  • Fine-tuning of subtle directional effects in H-bonding
  • Response to changing or heterogeneous molecular environments
  • Direct parameterisation against gas phase experimental data and QM results
  • Consistent treatment of intra- and intermolecular polarisation through a physically motivated damping scheme for local polarisation effects
  • Bond-angle cross terms
  • Wilson-Decius-Cross decomposition of angle bending in-plane and out-of-plane components
  • "Softer" buffered 14-7 van der Waals form 

The contributions that EPCC, together with the Software Sustainability Institute, will be making to the project are:

  • To provide efficient parallel (hybrid OpenMP / MPI) implementations of algorithms needed to be able to use the AMOEBA force field parameterisation on high-performance computing clusters
  • To test and validate these algorithms in TINKER but also to promote interoperability with other packages (Amber, DL_POLYONETEP, and Q-Chem) in order to promote uptake.

All of this will be done using an open development process to build a community around those packages that implement AMOEBA and variants of this model, which, in the long term, will make the future development of this force field self-sustaining. This will also make it easier for AMOEBA to be adopted by other software packages thus growing the community that can exploit this method.

This international partnership consists of members from EPCC at the University of Edinburgh, the UK Software Sustainability Institute, the University of Southampton, Daresbury Laboratory and from the US we have the University of California (Berkeley), Rutgers University, Claremont Colleges, Washington University in Saint Louis and New York University. The project started in April 2013 and runs for three years.

For further information, visit the APES project website.