ver_ http://www.ks.uiuc.edu/Research/gpu/files/siam2019-softnextgenplatforms-stone.pdf
Introduction to LAMMPS
In this video I give a short introduction to the LAMMPS simulation package. I will explain how LAMMPS can help you to run your molecular dynamics simulations faster and easier. I will also run a simple simulation with LAMMPS. The example LAMMPS input file can be found here:
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Locating Binding Sites in Protein Structures
Paul Labute and Martin SantavyChemical Computing Group Inc.Introduction | Methodology | Results | Summary | References Introduction Active sites in proteins are usually hydrophobic pockets that involve sidechain atoms. It is non-trivial to quantify this rule of thumb. Methods such as [Goodford 1985] or [Miranker 1991] use interaction energies between the receptor and different probes in an […]
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caver 3.0 Tunnels and channels
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a […]