Woodcock Group at USF

Hi All,

I am going to start using this blog as a way to communicate the exciting news that is coming out of the Woodcock Research Group at USF. 

Stay tuned for more.... 

CHARMM
(Chemistry at HARvard Macromolecular Mechanics):

• is a versatile and widely used molecular simulation program with broad application to many-particle systems
• has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments
• provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities
• is useful for a much broader class of many-particle systems
• can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models
• has been ported to numerous platforms in both serial and parallel architectures

---

CHARMMing: CHARMM INterface and Graphics

CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as Jmol for visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. Below is a partial list of functionality that currently is incorporated into CHARMMing.org:

• A CHARMM tutorial that has been specifically designed for novice CHARMM users
• PDB/CRD reader and input script generator
• Integrated molecular graphics
• Integrated simulation tools (i.e. minimization, solvation, dynamics)
• Automatic topology generation

CHARMMing was developed by the Laboratory of Computational Biology. Planning and development were done by:

* Rishi Singh
* Tim Miller
* Jeff Klauda
* Milan Hodoscek (GENRTF)
* H. Lee Woodcock *

With special thanks to:

* Bernard Brooks
* Rick Venable
* Xiongwu Wu

---

CHARMM Tutorial
Rishi P. Singh, Benjamin T. Miller, Jeffery Klauda, Xiongwu Wu, and H. Lee Woodcock

A tutorial/introduction to the use of CHARMM has been created and published on the web (CHARMM Tutorial). In addition, this has been integrated into CHARMMing. This tutorial provides conceptual foundations to molecular simulation techniques such as energy minimization, solvation, molecular dynamics, and the use of periodic boundary conditions that are implemented in CHARMMing. Thus CHARMMing may be used as an introduction to molecular simulations in general and CHARMM in particular with the tutorial serving as a manual.

First Post

Me, my wife and Gracie (my dog).



Gracie...



Gracie doing what she does best! :-)


Hello,

This is my first post. I will post more later, but have a look at my homepage (link on the right) and let me know what you think.

Cheers,
Lee