GROMACS molecule & liquid database

InVerDa - The Liquid Database

Multiple applications, which share one common database, will evolve over time by their very nature. Often, former versions need to stay available, so database developers find themselves maintaining co-existing schema versions of multiple applications in multiple versions—usually with handwritten delta code—which is highly error-prone and explains significant costs in software projects. We showc...

GROMACS: Fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance...

SMPDB: The Small Molecule Pathway Database

The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in clinical metabolomics, transcriptomics, proteomics and systems biology. SMPDB pro...

Note: Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS.

Improved GROMACS Scaling on Ethernet Switched Clusters

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...