1. Overview
============
This directory contains all files for a large set of tutorials on CHARMM
analysis tools. All examples are based on analyzing the solveted PDB structure
and a short (10 ps) MD trajectory of protein G B1 domain in a cubic box of 
TIP3P water. The files required for the MD simulation are in tutorial
"CHARMM-md-tip3p".

NOTE: please refer to the lecture note and html page for details. All input
      scripts contain aditional comments on various aspects of the demos.

Jianhan Chen (jianhanc@ksu.edu)

2. Files Descriptions
======================
2.1 common files for all tutorials (locate in the main directory)
---
toppar/:	contains the topology and parameter files (force field)
3gb1_solv.psf  	protein structure file (PSF) of the solvated system (protein + water)
3gb1_solv.pdb   equilibrated coordinates of the solvated system
nptprod.dcd     a 10 ps CHARMM binary trajectory file (for Intel Mac)

2.2. charmm input scripts for various demos (locate under directory: inputscripts/) 
---
orient.inp                      Reorient/recenter the trajectory, and remove solvent 
rmsd-singlepdb.inp		RMSD between two structures
rmsd-rgyr-traj-correl.inp	Extract RMSD and Rg from a trajectory using CORREL
rmsd-rgyr-traj-corman.inp       Extract RMSD and Rg from a trajectory using CORMAN and loop
hbond.inp                       H-bond analysis of a single structure, and the trajectory
2nd-structure.inp               Secondary structure analysis of a structure and trajectory
phi-psi-dist.inp                Extract phi/psi distributions from a trajectory
solvent.inp			Analysis of solvent structure and dynamics
nmr.inp                         NMR relaxation analysis, and relaxation time & order parameters 
trp-anisotropy.inp		Time-dependent fluorescence anisotropy of Trp
cluster.inp                     Clustering structures using CORREL

2.3. Sample analysis results: (locate under directory: data/)
---
*.dat	      data produced by the above analysis scripts
*.gnu	      gnuplot scripts for ploting and viewing some of the results
alldata.tgz   a TAR/GZ file that contains a copy of .dat and .gnu file
	      Will untar/unzip to a separate directory; can be used to as references 
	      for examining your own analysis.

2.4. Other files (locate in the main directory)
---
play.vmd      	      a vmd state file to view the trajectory 
play_protein.vmd      a vmd state file to view the extract protein only trajectory
3gb1_ini.pdb	      regularized PDB file of 3gb1 alone (for viewing protein trajectory) 

3. How to run the analysis (see the html page for more details)
==========================
In the main directory ( CHARMM-analysis/), run:

> $CHARMMEXEC < inputscripts/INPUT_SCRIPT_NAME | tee OUTPUT_FILE_NAME

(tee is a command that bifurcates output to a file and the terminal)