Generalized solvent boundary potential for computer simulations

Generalized solvent boundary potential for computer simulations

Efficient solvent boundary potential for hybrid potential simulations.

A common challenge in computational biophysics is to obtain statistical properties similar to those of an infinite bulk system from simulations of a system of finite size. In this work we describe a computationally efficient algorithm for performing hybrid quantum chemical/molecular mechanical (QC/MM) calculations with a solvent boundary potential. The system is partitioned into a QC region wit...

Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations

An approach is developed to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster. A rigorous theoretical formulation is given for the solvent boundary potential which takes the influence of the surrounding bulk into account. The solvent boundary potential is the configuration-dependent solvation free energy of an effective clust...

Generalized characteristic relaxation boundary conditions for unsteady compressible flow simulations

We develop numerical boundary conditions for the compressible Navier–Stokes equations based on a generalized relaxation approach (GRCBC), which hinges on locally one-dimensional characteristic projection at the computational boundaries, supplemented with available information from the flow exterior. The basic idea is to estimate the amplitude of incoming characteristic waves through first-order...

Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations

Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both e...