Difference between revisions of "Rizzo Lab Information and Tutorials"
From Rizzo_Lab
(→GROMACS) |
|||
| Line 64: | Line 64: | ||
===error analysis=== | ===error analysis=== | ||
[[Blocked Standard Error of the Mean]] | [[Blocked Standard Error of the Mean]] | ||
| − | + | ||
== GROMACS == | == GROMACS == | ||
| Line 71: | Line 71: | ||
|- | |- | ||
|[[MD Simulation: Protein in Water]] | |[[MD Simulation: Protein in Water]] | ||
| − | |||
|- | |- | ||
|} | |} | ||
Revision as of 14:58, 31 May 2013
Contents
Visualization Software
Basic Linux Tools
Docking
Molecular Dynamics
| AMBER Tutorials | AMBER TI Tutorials | AMBER tricks |
| NAMD tutorial | NAMD Amber inputs | |
| per-residue energy decompositions | nonstandard residues prep | |
| ptraj |
error analysis
Blocked Standard Error of the Mean
GROMACS
| Compiling GROMACS on Cluster |
| MD Simulation: Protein in Water |
Monte Carlo
Analysis Tools
Databases
- NCI (ligand database)
- NIST (small molecule database)
- ZINC (ligand database)
- Families in the Protein Databank
- Automated Families generation from the Protein Databank
- Drug-like organic molecules
BlueGene
Conversion between file types
Setting up accounts
| Getting a BNL Account | Activating your Seawulf Account | Rotation students Wiki | Setting up RSA SecureID token |
