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Three New Tutorials Available

The Theoretical and Computational Biophysics Group (TCBG) is proud to highlight the release of three new tutorials, on the topics of building molecules using VMD, making virtual beads using a coarse-graining method, and network analysis methods for examining dynamic signaling in biomolecular systems:

• Molefacture: A Tutorial to Build and Edit Molecules (pdf, 4.7M) (required tutorial files [.tar.gz, 17k] [.zip, 21k], individual files)
  molefacture is a VMD plugin that has been designed to facilitate the construction and parameterisation of small molecules. It additionally provides a simple interface to prepare structures and files for free energy perturbation calculations using NAMD. This tutorial serves as a primer for structure building, modification and parameterization using the molefacture plugin of VMD. Prior knowledge of NAMD and standard molecular dynamics simulations is assumed. Requires VMD, NAMD, and Amber.
• Residue-Based Coarse-Graining (pdf, 10.1M) (required tutorial files [.tar.gz, 124M] )
  The tutorial reviews residue-based coarse-graining (RCBG), a method in which several atoms of a biological macromolecule are grouped together in a “virtual” bead (e.g., a single amino acid is represented by 2-5 beads). The reduction in degrees of freedom makes the model computationally efficient alternative to atomistic models, allowing for simulations to be run on larger systems and longer time scales. Requires VMD, NAMD 2.9 or higher. Tutorial works on Windows, Mac, and Unix/Linux platforms.
• Dynamical Network Analysis (pdf, 4M) (required files [tar.gz, 192M]) (network analysis code [tar.gz, 27M])
  This tutorial introduces several network analysis methods for examining dynamic signaling in biomolecular systems. The NetworkView plugin to VMD is used to display and manipulate representations of the networks projected onto the underlying molecular structures. The tutorial is designed such that it can be used by both new and experienced users of VMD, however, it is highly recommended that new users go through the "Using VMD" tutorial in order to gain a working knowledge of the program. Users will also need to download the free Carma software program for the tutorial. This tutorial should take about two hours to complete in its entirety.

Each tutorial provides text and files to be used along with TCBG's software programs VMD and NAMD, which are freely available for download from this website. For more tutorials see TCBG's tutorials page.