http://www.ks.uiuc.edu/Research/gpu/files/IUVR-VMD-Stone.pdf
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 […]
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CGenFF running simulations with other programs
Running simulations with other programs NAMD The following steps should allow for CGenFF to be used with NAMD: Download and unpack the latest CHARMM force field distribution Overwrite the main CGenFF topology and parameter files downladed in the previous step with the CGenFF version that is compatible with the toppar file(s) you got out of the CGenFF program […]
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Molecular Dynamics in 5 Minutes
This is a 5 minutes introduction to molecular dynamics simulation. Tools to generate initial state for your system: – LAMMPS lattice command: This command creates a 2D or 3D lattice. It supports a number of lattice types.