BioCoRE - A Tool-Oriented Collaboratory for Structural Biology

BioCoRE - Biological Collaborative Research Environment

BioCoRE - A Tool-Oriented Collaboratory for Structural Biology November 7, 2000 - The BioCoRE team is proud to release the NAMD Configuration File Generator today. The tool is accessible from BioCoRE -- Workbench -- NAMD Configuration File Generator.

The NAMD Configuration File Generator is a secure and reliable Web-based tool created using pure Java. The purpose is to help NAMD's users to create and edit NAMD input files.

Important note: in order to run NAMD Configuration File Generator your web browser doesn't normally have the permissions needed to create, read or save files to directories on your machine. You have to set your web browser up to be able to do this. You only need to set it up once, and you do this by importing a security certificate. For this to work, you need to be running Netscape (other browsers use different mechanisms for security certificates that we are not yet supporting).

To import the certificate, access BioCoRE -- Workbench -- VMD -- press the "Get Certificate" button. Then follow the instructions.

Please check the following features when you use NAMD Configuration File Generator: 

New -- Create a new NAMD Configuration File
Open -- Open an existing file on your machine
Save and Save as -- Error protection and saving files to your machine
ViewText -- Error protection and view the file
Exit -- exit the applet
About -- Describes the NAMD configuration file generator
Status-bar -- display the status of the applet.
All config file options are listed in tabs and grouped as: 
   
FORCE FIELD:
1. Input Files:
2. Basic Dynamics:
3. Space Partitioning:
4. Boundary Conditions:
ENSEMBLE:
1. Timestep:
2. Temperature Control:
3. Pressure Control:
INITIAL:
OUTPUT:
PROTOCOL:
1. Timestep:
2. Temperature Rescaling/Reassignment:
3. Steered Molecular Dynamics:
4. Interactive Molecular Dynamics:            
5. Tcl Interface:
ADDITIONAL:
1. Additional Parameters:
2. Comments:
Error protection:
Once a value (or path ) is set, the data type and arrangement will be checked by clicking on "ViewText", "Save" or "Save As..",

A pop-up window will show the number of errors in the file along with a description of each one.

Interaction among the parameters: Once you set a value for a parameter, it often affects other parameters (as determined by NAMD).

Default:
Default value will be set once a new file is created.

The applet was designed on Unix, so it currently looks better on a Sun box than anywhere else. We are working on making it look nice on other platforms.

Note: if it is the first time (only for first time) you resize the window after load the applet (or reload it) on Unix platform (never happened on Windows), the appplet will stop, destroy and then init. So your data that you typed in the interface could be destroied because the window is resized first time after the appletis loaded. It will be no problem after second(included) time resize it. It is the "feature" of Netscape on Unix. Therefore, the better way is: resizing the window first and then edit or modify you data after you load or reload the NAMDConfiguration File Generator.

Please sent your bug reports, suggestion or comments to biocore@ks.uiuc.edu or click on the link at bottom of applet window -- "Suggestions or Comments for NAMD Configuration File Generator".