1. Overview
============
This directory contains all files for three tutorials on running GBSW implicit 
solvent and implicit membrane simulations.

Jianhan Chen (jianhanc@ksu.edu)

2. Files Descriptions
======================

2.1 toppar/:	contains the topology and parameter files (force field)

top_all22_prot_cmap.inp: regular CHARMM22 topology file
par_all22_prot_gbsw.inp: parameter file contains a GBSW-specific CMAP
radius_gbsw.str:	 optimized input radii for GBSW peptide simulation

2.2 Input scripts:

gbsw_peptide.inp:	 sample script for peptide simulation with GBSW
gbswmemb1.inp:		 sample script for membrane simulation with GBSW
gbswmemb2.inp:		 sample script for GBSW membrane simulation with 
    			 symmetry imposed.

3gb1.pdb     		 regularized PDB:3GB1
1zll/:			 original PDB:1zll and convpdb.pl processed files
			 (see 1zll/conv.sh)

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

> $CHARMMEXEC < INPUT_SCRIPT_NAME | tee OUTPUT_FILE_NAME

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

4. Known bugs

It appears that the c35b2 with Mac OS X 10.5/gfortran compiled version (with core2 
compilor option) has a bug that leads to (random?) segment fault.

The input scripts run otherwise fine.