Difference between revisions of "Rizzo Lab Information and Tutorials"

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(Molecular Dynamics)
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== Molecular Dynamics ==
== Molecular Dynamics ==
{| cellpadding=0 width=90%
{| cellpadding=0 width=90%
|[[AMBER Tutorials]]
*[[AMBER Tutorials]]
|[[AMBER TI Tutorials]]
*[[AMBER TI Tutorials]]
|[[AMBER Lipid Tutorials]]
*[[AMBER Lipid Tutorials]]
|[[AMBER tricks]]
*[[AMBER tricks]]
*[[NAMD tutorial]]
|[[NAMD tutorial]]
*[[NAMD Amber inputs]]
|[[NAMD Amber inputs]]
*[[per-residue energy decompositions]]
*[[nonstandard residues prep]]
|[[per-residue energy decompositions]]
|[[nonstandard residues prep]]
*[[Blocked Standard Error of the Mean]]
|[[Blocked Standard Error of the Mean]]

Revision as of 12:05, 4 February 2019

Visualization Software

Basic Linux Tools


De novo Design using DOCK

Molecular Dynamics


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
Semester Checklist Wiki Editing
Stony Brook Joint Group Meetings in Computational Structural Biology Other Meetings Seawulf Cluster Assessment

Formating Word Documents

Formating your Thesis


Research Foundation


Legacy Info