Pathsampling short paths
If your initial connected path is short, and there weren't very many off-pathway stationary points found in the initial connection run, then you should think about the underlying energy landscape before pathsampling.
Go back to the GMIN run (or set one up!) and see what the energy range of all the minima found is (look at the file "energy" in your favourite graphing program). Also look at "markov" and the overall acceptance ratio for the run to see how effective the chosen input settings were. Look at the structures of the x lowest-energy minima found (lowest[1-x].pdb) to examine the structural range covered. You could try rerunning with a higher temperature, or with more final quenches, to explore more of the landscape.
Multiple conformational families
If you have minima corresponding to more than 2 distinct conformational families (for example, amongst the structures found in the GMIN run) then you can set up additional, separate OPTIM connection-making runs, as before when Finding an initial path with OPTIM and starting up PATHSAMPLE, between all the pairs of end points of interest. However, when you have the path.info file(s) from OPTIM you may not want to use them to start a new database -- instead, you can add them (one at a time) to an existing PATHSAMPLE kinetic transition network (KTN) with a pathdata file like this:
ADDPATH path.info.add ADDTRIPLES TRIPLES NATOMS 33 ETOL 1.0D-4 ITOL 1.0D1 GEOMDIFFTOL 1.0D-1 TEMPERATURE 0.592 CYCLES 0 PERMDIST AMBER9
Run this PATHSAMPLE job in the directory containing the existing KTN, after having copied the relevant OPTIM path.info to ./path.info.add . Note that this run will NOT change or add anything to the min.[A,B] files. Also, DON'T RUN an ADDPATH job when a different kind of pathsample job is also running in the same directory - that would potentially mess up the database files! In fact that's a general rule - don't run multiple PATHSAMPLE jobs at the same time in the same directory.
Systematically increasing the number of connections per minimum
Increasing the overall connectivity of the KTN using CONNECTREGION
In the directory containing the files from the pathsampling runs so far, edit pathdata to include only the following:
TRIPLES NATOMS 33 ETOL 1.0D-4 ITOL 1.0D1 GEOMDIFFTOL 1.0D-1 TEMPERATURE 0.592 CONNECTIONS 1 COPYFILES perm.allow min.in coords.prmtop coords.inpcrd EXEC /home/jmc49/bin/A9OPTIM CONNECTREGION 1 2 CYCLES 50 PAIRLIST 1 PERMDIST AMBER9
and submit this PATHSAMPLE job, on multiple processors if available (add a JOBSPERNODE <n> or CPUS <n> line to pathdata as appropriate). Set EXEC and CYCLES appropriately - CYCLES tells PATHSAMPLE how many cycles of OPTIM jobs should be run, where the number of parallel, independent OPTIM jobs per cycle is determined by the JOBSPERNODE/CPUS settings and the number of compute nodes you are running the actual PATHSAMPLE job on. Note that a CONNECTREGION run only needs an odata.connect as far as OPTIM data files are concerned.
The result of such a run should be an expanded KTN, i.e. more entries in min.data, ts.data and the corresponding points files.