Rizzo Lab Information and Tutorials

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Visualization Software

Basic Linux Tools

Unix vi sed - Stream Editor in Unix
Stupid awk tricks Ways to remove the first line PBS Queue
gdb (GNU Debugger) Common Errors - ctrl M C Shell Scripting
Unix find Which Unix Distribution? rsync


DOCK Tutorials Testset Protocols Scoring Functions Sampling Methods
ZINC Database Installing DOCK

Molecular Dynamics

AMBER Tutorials AMBER tricks
NAMD tutorial NAMD Amber inputs

NAMD and DOCK on BlueGene

Monte Carlo

Analysis Tools



Get time estimate for free blocks Get Job ids to use for llcancel Get time for job completion
Submitting BlueGene Jobs Compiling Applications for BG/L BlueGene LoadLeveler Jobs with Multiple Steps (Chain Jobs)

Conversion between file types


X-Win32 CVS Commands Ethernet Cables
Getting a BNL Account Getting a Seawulf Account Sequence alignment
Visiting BNL Making images for publication Lab-designed code and programs
scp files from cluster to NYBlue Setup ssh tunnel to NYBlue fen Server Administration
Amber on Seawulf (compilation) NAMD on Seawulf Dell 5110cn Printer Rotation students Wiki


Research Foundation