While alchemy has been given up for a long time as a subject in Chemistry, we as theoretical chemists, can still perform simulations of alchemical transformations and learn interesting details about the differences in the binding free energy (binding strength) with very high accuracy. I spent some time of my life in the beautiful French city of Nancy developing the method to perform alchemical free energy calculations using the state-of-the-art molecular dynamics code NAMD (That is a mnemonic for Not Another Molecular Dynamics!)

Here are the pages from the NAMD manual that detail this feature: http://www.ks.uiuc.edu/Research/namd/current/ug/node34.html

There is also a tutorial to guide in setting up such a simulation: http://www.ks.uiuc.edu/Research/namd/tutorial/AlchemicalFEP.pdf

I am currently involved in teaching a course on 'Molecular Modeling and Molecular Dynamics'. Here is the link to the website I maintain for this course.

http://sdixit.web.wesleyan.edu/wescourses/2006s/chem388/01/mdcourse

You would find the lecture slides and a set of exercises and tutorials to get you started in MD/MM.

Our group was involved in teaching a course on 'Bioinformatics: Genomics and Proteomics'. Enter the realm of Bioinformatics!

Here are some links from my bookmark that you might find interesting (beware some of these links might be outdated):

Web Links of Interest

Software

AMBER

CHARMM

GROMOS

NAMD - Scalable Molecular Dynamics

Sigma - Jan Hermans

MMTK Home Page

CACHE Molecular Modeling

The Babel Home Page

The Open Babel Home Page

 

 

VMD - Visual Molecular Dynamics

Chimera Home Page

PyMOL Home Page

Graphics Interface for OpenMol (gOpenMol)

 

MOLMOL - MOLecule analysis and MOLecule display

Deepview: Swiss PDB Viewer

 

The MDL Chime Site

History of Molecular Visualization

PDB to MultiGif Page

Structure Morphing Movie

Molecules in Motion Interactive Tutorials

MD techniques

Introduction to Macromolecular Simulation: P.J.Steinbach

Forcefield nitty gritty: Bookmarks of M.B.Gillies

Fundamentals of Molecular Interactions and Dynamics: R.H.Templer

Charmm MD Tutorial: R.Stote

Statistical Thermodynamics of Materials: Veytsman & Kotelyanskii

MD Course Notes: Frenkel and Smith

Molecular Modeling and Theory: E.J.Maginn

DNA Star: Yliu

MDTC Tutorial

Hydration

Kevin Cowtan's Picture Book of Fourier Transforms

Molecular Biology Notebook Courses

Alex MacKerell Home Page : Charmm FF Development

Documentation

Annotated CHARMM .doc Index

CHARMM .doc Home

CHARMM Documentation

Documentation for the HOLE_ 3.0 Control Cards

Index to the MDTC Home Pages

MSI OnLibrary

NUCPLOT manual

Uppsala Software Factory - XPLO2D Manual

X-PLOR On-line Manual

ROAR Manual