Expanding the kinetic transition network with PATHSAMPLE (CHARMM)

You can carry on expanding the database of stationary points with a variety of approaches in PATHSAMPLE, analysing as you go along in a number of ways too.

Make sure you're working in a directory containing:

• min.A, min.B
• min.data, ts.data
• points.min, points.ts
• pathdata
• perm.allow
• input.crd
• odata.connect

Take care not to delete odata.connect with odata.[0-9]* files that accumulate from the OPTIM jobs PATHSAMPLE sets off.

See also the PATHSAMPLE tutorials.

However, note that if the initial pathway and starting database of minima are small (say a pathway of < 10 transition states) then the usual pathsampling approaches (SHORTCUT, FREEPAIRS, UNTRAP) won't be effective, as they are designed to optimize long winding paths :-) Some alternative options are discussed in pathsampling short paths (CHARMM).

You can make a disconnectivity graph (a.k.a. tree) on the PATHSAMPLE database at any point, see DisconnectionDPS for an intro to the program we use.

The source code is in the trunk of the SVN repository, in subdirectory /DISCONNECT/source/ . There's a Makefile. To run the resulting program, in the directory where you did the pathsampling, give the command:

<path-to-executable>/disconnectionDPS 

and then have a look at tree.ps with gv or similar.