TE 589P

From WolfWikis

Overview

Molecular Simulations for Science and Engineering is intended to be a compilation of resources for molecular modeling for both the NCSU Molecular Simulations course (TE589M) and the Pasquinelli Research Laboratory.

NOTES TO CONTRIBUTORS

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Works in Progress

Remote Access 101 --Alex R 13:56, 6 November 2007 (EST)

General Resources

[1] http://www.chem.swin.edu.au/courses/swin/sc680/index.html

Visualization Software and Graphical User Interfaces

Main article: Visualization Software (Chemistry)

Some examples of Visual Computational Chemistry Software are Visual Molecular Dynamics, , MolStart, Ghemical, Extensible Computational Chemistry Environment, QUANTA, MolScript, Raster3D, and Coot (Software).

Alex R 10:51, 25 July 2007 (EDT)

Syamal Tallury 20 May 2008 (EDT)

Molecular Builders with Graphical User Interface

These are some molecular builders which have decent graphical user interfaces:Maestro, Aten

Syamal Tallury 20 May 2008 (EDT)

Modeling Techniques

--Alex R 16:40, 23 July 2007 (EDT)

Molecular Mechanics

Main article: Molecular Mechanics

Molecular Mechanics as presented by the National Institute of Health's Guide to Molecular Modeling.

--Alex R 13:44, 20 July 2007 (EDT)

Quantum Chemistry

Main article: Quantum Chemistry

Quantum Mechanics - NIH Guide to Molecular Modeling

An introduction to quantum chemistry specifically as it relates to the GAMESS quantum chemistry package.

--Alex R 10:11, 23 July 2007 (EDT)

Molecular Dynamics

Main article: Molecular Dynamics

DL_POLY is a general purpose serial and parallel molecular dynamics simulation package.

CHARMM

--Alex R 16:03, 23 July 2007 (EDT)

Monte Carlo Simulations

Main article: Monte Carlo Simulations

Put stuff here

Brownian Dynamics

Main article: Brownian Dynamics

Put stuff here

Hybrid Methods

Main article: Hybrid Methods

Put stuff here

Databases

Main article: Databases (Chemistry)

Molecule structures are stored in files in online databases for use by scientists all over the world.

The Cambridge Structural Database - The world repository of small molecule crystal structures

Most of the molecules you will be dealing with have already been constructed into a PDB (Protein Databank) file. There used to be several protein databanks on different continents, but now there is the Worldwide Protein Databank as a single database for all PDB files.

The closest access to NCSU is the RCSB (USA) mirror.

RCSB Protein Databank (Polypeptides and polysaccharides)

Nucleic Acid Database- a repository of three-dimensional structural information about nucleic acids. (Oligonucleotides)

Inorganic Crystal Structures Database (Inorganic structures)

CRYSTMET contains chemical, crystallographic and bibliographic data together with associated comments regarding experimental details for each study. (Metals and alloys)

National Institute for Materials Science Materials Database

Drug Bank

--Alex R 10:14, 25 July 2007 (EDT)

Lab Procedure

README

While working, it's a good idea to have a text editor open so you can record anything important that you do. This is any information required to duplicated what you have done, as well as other general info for anyone else that is looking in your directory. So if you have particularly confusing file names, define and explain those in the readme file.

Another variation is the DONTREADME file, which everyone reads anyway because of reverse psychology.

File Names

Your file names should be HUMAN READABLE, so that anyone can look in your directory and understand what is there. Also, you should have some kind of definition of the file and how you used it in your README or DONTREADME files.

File Permissions

If you are continuously using a file or modifying it and saving different versions, its a good idea to change the file permissions on it. Make files that are NOT going to change again (soon) READ-ONLY.

For Windows Users

Right click on the file and select "Properties" at the bottom of the list. The 'Properties' window should pop up. Under the 'General' Tab in the 'Attributes' section check the Read-Only box (this should be at the bottom of the window).