We investigated the prerequisites for decent scaling of the GROMACS 3.3 molecular dynamics (MD) code [1] on Ethernet Beowulf clusters. The code uses the MPI standard for communication between the processors and scales well on shared memory supercomputers like the IBM p690 (Regatta) and on Linux clusters with a high-bandwidth/low latency network. On Ethernet switched clusters, however, the scali...

ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR),...

The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize stati...

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and angles. This allows us to extend length of interval therefore range physical phenomena that afford simulate. We examine existing algorithms software for solving nonlinear constraint equations in parallel explain why it is necessary advance state-of-the-art. present ILVES-PC, a new a...

GridMAT-MD is a new program developed to aid in the analysis of lipid bilayers from molecular dynamics simulations. It reads a GROMACS coordinate file and generates two types of data: a two-dimensional contour plot depicting membrane thickness, and a polygon-based tessellation of the individual lipid headgroups. GridMAT-MD can also account for proteins or small molecules within the headgroups o...

In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PE...