1. Computer simulation studies of forced rupture kinetics of
“hydrophobic bonds” between hydrocarbon chains
Valeri Barsegov, Department of Chemistry, University of Massachusetts Lowell
I. Although the nature of hydrophobic forces is well understood, little is known about the kinetics of hydrophobic interactions. We proposed to address this problem by carrying out all-atom Molecular Dynamics (MD) simulations of the formation and rupture of “hydrophobic bonds” between short hydrocarbon chains (C16H34) in explicit water. However, to compare the results of computer simulations, obtained in reasonable wall-clock time, with recent atomic force microscopy (AFM) data, requires using a pulling force, applied to rupture a hydrophobic bond (C16H34-C16H34 contact), that is ramped up 104-times faster than the mechanical force used in AFM experiments (pulling speed of ~1-10μm/s). To overcome this limitation, in the first year of the project we have developed an implementation of all-atom MD simulations in explicit water on Graphics Processing Units (GPUs), which has been made into a standard CUDA code (Compute Unified Devise Architecture from NVIDIA, extension of C-language).
II. We have tested extensively the numerical stability and accuracy of the CUDA code, which utilizes OPLS force-field and SPC/E water model. We have compared the performance of our MD-GPU program with standard implementations of all-atom MD simulations on a Central Processing Unit (MD-CPU), such as GROMACS, and found that
results of MD simulations on GPUs compare well with the results of MD simulations on CPUs;
use of MD-GPU program allows to obtain a ~10-fold computational speedup compared with MD-CPU implementations.
III. The GPU based implementation of MD simulations will enable us to implement slower pulling speeds that are closer to the ones used in AFM experiments (and weaker forces), in order to study weak hydrophobic bonds that are intrinsically unstable.
IV. In the second year of the project, the developed MD-GPU software will be used (1) to probe the kinetics and thermodynamics of hydrophobic bonds, (2) to map the free energy landscape underlying formation and rupture of hydrophobic contacts, and to resolve microscopically the contact minimum (CM) state and the solvent-separated minimum (SSM) state.