Nowadays the state of the art Density Functional Theory (DFT) codes are based on local (LDA) or semilocal (GGA) energy functionals. Recently the theory of a truly nonlocal energy functional has been developed. It has been used mostly as a post DFT calculation approach, i.e. by applying the functional on the charge density calculated using any standard DFT code, thus obtaining a new improved value for the total energy of the system. Nonlocal calculation is computationally quite expensive and scales as N^2 where N is the number of points in which charge density is defined, and a massively parallel calculation is essential for a wider applicability of the new approach. In this article we present a code which acomplishes this goal.

We study the chemisorption of CO molecule into sites of different coordination on (111) surfaces of late 4d and 5d transition metals. In an attempt to solve the well-known CO adsorption puzzle we have applied the relatively new vdW-DF theory of nonlocal correlation. The application of the vdW-DF functional in all considered cases improves or completely solves the discrepancies of the adsorption site preference and improves the value of the adsorption energy. By introducing a cutoff distance for nonlocal interaction we pinpoint the length scale at which the correlation plays a major role in the systems considered.

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.