THIS DOCUMENT IS AN INCOMPLETE DRAFT
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 NAST Instability Evasion Routine (NASTIER) 	ver. 0.7
 July 11, 2010 - Ajaykumar Gopal
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WHY MAKE THIS TOOL?
1) In order to get statistically reliable dynamic information about large RNAs (>500nt) with minimal constraints, you need longer MD trajectories (~10^9 steps). The larger the molecule gets, the more long-timescale fluctuation modes it possesses, leading to gradual but large (as much as 50%) changes in physical quantities. For example the distance between two nucleotides far apart in sequence index in a 1000nt sequence may fluctuate by over 30% during 10^8 simulation steps. To find the correct trajectory lenght for your molecule, you'll probably need multiple runs and a manager to locate all the files generated. 

2) RNAs longer than 500nt typically contain large domains. The slow collective motions of domains with respect to each other can lead to sharp increases in local stresses, causing explosions in the simulation. When this happens, it is not sufficient to retrace back to the beginning of the current report interval and start a new run. Doing this will likely lead to another explosion. Often, one needs to retrace a few or several more reports (depending on their frequency) to return to a non-explosive path. Doing this manually is not realistic, because it involves manually extracting PDB snapshots from failed runs and inputing these into the next run hundreds of times. (It is not uncommon for a 1000nt sequence to explode between 500-1000 times on the way to 10^9 steps.)
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THE SOLUTION: NASTIER
This tool automates an explosion evasion routine, which catches exploded runs, retraces a customizable number of reports and starts the next run, proceeding until the desired number of steps are computed. It also automatically collates and concatenates the results into a single trajectory file to provide a coherent and seamless output for subsequent analysis.
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SYSTEM REQUIREMENTS
1) At this time, NASTIER can only be used on machines with access to a terminal capable of running the bash shell. 
-- LINUX/UNIX: Most linux distributions offer the bash shell as an option or the default shell for a command-line terminal. 
-- Windows PC: Install Cygwin and enable the bash package. http://www.cygwin.com
-- MAC OSX: Bash is the default shell for the OSX "Terminal" utility. Details at http://developer.apple.com/internet/opensource/opensourcescripting.html

2) NAST-0.8 or later must already be installed and working reliably on smaller RNAs.
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INSTALLATION INSTRUCTIONS (Draft)
1) Determine the path to compatible python binary for nastier.cfg.
2) If running nastman for multiple folders, add script to path.
3) Ensure script shebang is accurate in nastier.sh (which env or bash)
4) Ensure 755 permissions for nastier.sh (read+exec).
5) Dependencies (Attn: Mac and Cygwin): date, awk, sed, grep, cat
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RUNNING NASTIER (Draft)
0) Generate an initial PDB file using RU or a short NAST run.
1) Enter NAST Parameters in nast.py
2) Change NASTIER configuration if required (initial run/retrace#)
3) Syntax for run in current folder: sh nastier.sh OR ./nastier.sh
4) Names of temporary files not to change/delete during run:
output.pdb, traj.pdb, input.pdb, nast.py
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GOT PROBLEMS? (Draft)
1) Discussion board:
2) Bug Report/Feature Request: 
3) Contact Form: https://simtk.org/users/ajzz