A GPU-accelerated immersive audiovisual framework for interaction with molecular dynamics using consumer depth sensors. Faraday Discussions, 169. pp. 63-87. ISSN 1359-6640 Available from: http://eprints.uwe.ac.uk/23115We recommend you cite the published version. The publisher's URL is: http://dx.doi.org/10.1039/C4FD00008K Refereed: Yes First published online 19 Mar 2014Disclaimer UWE has obtained warranties from all depositors as to their title in the material deposited and as to their right to deposit such material. UWE makes no representation or warranties of commercial utility, title, or fitness for a particular purpose or any other warranty, express or implied in respect of any material deposited. UWE makes no representation that the use of the materials will not infringe any patent, copyright, trademark or other property or proprietary rights.UWE accepts no liability for any infringement of intellectual property rights in any material deposited but will remove such material from public view pending investigation in the event of an allegation of any such infringement. PLEASE SCROLL DOWN FOR TEXT.A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors † With advances in computational power, the rapidly growing role of computational/ simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360 spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360 atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Internally contracted multireference coupled cluster (icMRCC) theory is embedded within multireference perturbation theory (MRPT) to calculate energy differences in large strongly correlated systems. The embedding scheme is based on partitioning the orbital spaces of a complete active space self-consistent field (CASSCF) wave function, with a truncated virtual space constructed by transforming selected projected atomic orbitals (PAOs). MRPT is applied to the environment using a subtractive embedding approach that also allows for multilayer embedding. Benchmark calculations are presented for biradical bond dissociation, spin splitting in a heterocyclic carbene and hydrated Fe(II), and for the super-exchange coupling constant in solid nickel oxide. The method is further applied to two large transition metal complexes with a triple-ζ basis set: an iron complex with 175 atoms and 2939 basis functions, and a nickel complex with 231 atoms, and 4175 basis functions.

We have used a generalised coherent state resolution of the identity to map the quantum canonical statistical average for a general system onto a phase-space average over the centre and width parameters of a thawed Gaussian wave packet. We also propose an artificial phase-space density that has the same behaviour as the canonical phase-space density in the low-temperature limit, and have constructed a novel Nosé-Hoover looped chain thermostat that generates this density in conjunction with variational thawed Gaussian wave-packet dynamics. This forms a new platform for evaluating statistical properties of quantum condensed-phase systems that has an explicit connection to the time-dependent Schrödinger equation, whilst retaining many of the appealing features of path-integral molecular dynamics.

We present a mapping of quantum canonical statistical averages onto a phase-space average over thawed Gaussian wave-packet (GWP) parameters, which is exact for harmonic systems at all temperatures. The mapping invokes an effective potential surface, experienced by the wave packets, and a temperature-dependent phase-space integrand, to correctly transition from the GWP average at low temperature to classical statistics at high temperature. Numerical tests on weakly and strongly anharmonic model systems demonstrate that thermal averages of the system energy and geometric properties are accurate to within 1% of the exact quantum values at all temperatures.