MOIL - A Public Domain Molecular Modeling Software
	Description	Downloads	Documents	Examples	WebMoil

Description

MOIL is a molecular modeling software, which is in the public domain, and is written in the group of  Ron Elber.

In addition to widely available features, such as energy calculations, minimization and calculations of classical trajectories, MOIL has a few special features that are difficult to find in general modeling packages:

• Locally Enhanced Sampling (LES);
• Long time dynamics algorithms, the stochastic difference equations SDET and SDEL, to extend significantly the time scale of simulations;
• The Landau-Zerner model to dissociation and recombination of ligands, and curve crossing;
• Graphic User Interface for a wide range of moil applications on a Windows desktop. This interface enables direct calculation on a desktop, on a Windows cluster, and on properly configured web servers. 

The new release also includes a significantly enhanced molecular viewer for Windows with numerous options of drawing and printing individual structures, set of structures, and displaying dynamics. 

For more documents please click here.

Downloads and Installation

The most current version of MOIL is MOIL9.1. This is the MOIL9 core code plus the Graphic User Interface changes. If you're interested in previous versions of MOIL, please click here.

1. Download and run the MOIL installation program Moil901Setup.exe (http download);
2. Download and run the Tcl/Tk installation program ActiveTcl8.4.4.0-win32-ix86.exe
   (Tcl/Tk is required for the use of the Graphic User Interface) .

1. Download the MOIL source code moil901.tar.gz (http download);
2. Unpack it with command "gzip -cd moil901.tar.gz | tar xv" in the download directory;
3. Go to the moil9/moil.source directory and compile the code with the Makefile
   (you may need to adjust some options in the Makefile) .

Now MOIL is ready to run.

Examples

• Some output samples of MOIL examples with corresponding graphics;
• An example of how to use the CBSU resources with the built-in web-client of MOIL.

WebMoil

With build-in web client in the GUI, MOIL9.1 can run molecular simulation jobs on remote web servers. Currently, MOIL default WebMoil server is the CBSU cluster at the Cornell Theory Center. The MOIL web server configuration package will be made available later. Clik here for CBSU cluster resource information.

To use WebMoil, you just download and install the MOIL and Tck/Tk as indicated above, set the parameters just like you would run MOIL on desktop, then click on "Run on Web" command button in the bottom of a worksheet. With your email information, the job request will be sent to WebMoil server. When the job is completed, you will get an email notification for downloading results.

MOIL web submission is limited to 10 processors @1 hour each and should be used for testing purposes only. More resources may be made available from the CBSU by sending an email request to cbsu@tc.cornell.edu. In your e-mail please describle briefly your project run and specify the resources you need.

Bug Report

Please send any bug reports and sugguestions to moil@tc.cornell.edu.

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