Catdcd Interface

CatDCD is a versatile tool that can be cumbersome to use for non-experienced users as it is available primarily through a command line interface. The purpose of this program is to provide an easy to use interface for CatDCD and make it much simpler to perform batch tasks to process lots of data. For questions, comments, or the source code, send an email to the developer.

Running the Application:
The first time running the application, it is imperative to run the configuration editor to make sure that the folder paths are correct.
Configuration
To edit/check the configuration parameters click on the runtime menu Tools>Configuration or use the shortcut key (Command-E)
There are three configurable parameters:
CatdcdExecutableFolderLocation
The location of catdcd. This can either be the version distributed with VMD (show package contents - Contents/vmd/plugins/MACOSXX86/bin/catdcd5.1)
VMDStartupApplicationLocation
The location of the VMD startup.command file on Mac. The default location on a Mac is, for example /Applications/VMD\ 1.9.2.app/Contents/MacOS/startup.command
TCLScriptFolderLocation
This is really just the location of the getAtomSeelctionIndices.tcl script used to index the atom selection in that operational mode.
Normal Usage
The file path controls are all compatible with drag and drop functionality so the user can drag pdb, dcd, or other files directly into the GUI controls and it will update the file path automatically.
Select PDB file
Select DCD file(s)
Decide operational mode:
1to 1 will map an output dcd file to every input to is useful execute multiple runs at once.
Many to 1 will concatenate the dcd files into a single output trajectory. Useful for combining different simulations together.
Set frame parameters
Determine whether or not to index. If so, input desired VMD compatible atom selection (as seen from the command line. For example, one must escape certain characters e.g. "type C1\' "
Select output file(s) (Note: an additional folder with the report name will be created to contain the analysis output)
If desired, request a log file (it will have the same file name as the first output file with a different file extension.
Execute
Rinse & Repeat
Quit when complete