Difference between revisions of "Rizzo Lab Information and Tutorials"

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Line 68: Line 68:
  |[[Compiling GROMACS on Cluster]]
  |[[Compiling GROMACS on Cluster]]
|[[Simple Protein in Water MD]]
  |[[Protein-Ligand Complex MD]]
  |[[Protein-Ligand Complex MD]]
  |[[Membrane Protein MD]]
  |[[Membrane Protein MD]]
  |[[TI: Mutating Ligand to Nothing]]
  |[[TI: Mutating Ligand to Nothing]]

Revision as of 14:29, 19 July 2011

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
MPICH Secure Shell (ssh) Archiving old data


DOCK Tutorials Testset Protocols Scoring Functions Sampling Methods
ZINC Database Installing DOCK Optimize Polar Hydrogens Virtual Screening Protocol
Sphere Generation DOCK Compilation

Molecular Dynamics

AMBER Tutorials AMBER TI Tutorials AMBER tricks
NAMD tutorial NAMD Amber inputs
per-residue energy decompositions nonstandard residues prep

NAMD and DOCK on BlueGene

error analysis

Blocked Standard Error of the Mean autocorrelation function


Compiling GROMACS on Cluster
Simple Protein in Water MD Protein-Ligand Complex MD Membrane Protein MD
TI: Mutating Ligand to Nothing TI: Mutating Ligand to Ligand Steered MD / Umbrella Sampling

Monte Carlo

Analysis Tools



Setup ssh tunnel to NYBlue fen Get time estimate for free blocks Get Job ids to use for llcancel
Submitting BlueGene Jobs Compiling Applications for BG/L LoadLeveler Chain Jobs
scp files from cluster to NYBlue Get time for job completion

Conversion between file types

Setting up accounts

Getting a BNL Account Activating your Seawulf Account Rotation students Wiki Setting up RSA SecureID token


X-Win32 CVS Commands Ethernet Cables Sequence alignment
Visiting BNL Making images for publication Lab-designed code and programs Server Administration
Amber on Seawulf (compilation) Cluster compilations NAMD on Seawulf Dell 5110cn Printer


Research Foundation