CHARMM is a popular molecular dynamics code for computational biology. For many CHARMM applications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this technical report, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We ...

CHARMM is a popular molecular dynamics code for computational biology. For many CHARMM applications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this paper, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We identify th...

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational flexibility. Normal modes from four simple elastic network model potentials and from the CHARMM force field are calculated for a ...

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncert...

An assessment of nine scoring functions commonly applied in docking using a set of 189 protein-ligand complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function used in AutoDock, the three scoring functions implemented in DOCK, as well as three scoring functions implemented in the CScore module in SYBYL (PMF, Gold, ChemScore)...

This paper investigates the mechanism of water transportation through aquaporin-4(AQP4) of ratbrain cells by means of molecular dynamics simulation with CHARMM software. The AQP4 wasembedded into a bilayer made of Dimystroilphosphatylcholine (DMPC). The results illustrate thatwater molecules move through AQP4's channel with change of orientation of oxygen of eachwater molecule.