Optimising a path

Under construction...

Once a full connection has been thought to be made, it is best to verify that there is indeed a connection. Run another PATHSAMPLE calculation with DIJKSTRA 0 and CYCLES 0. A common gotcha is a too high of a MAXTSENERGY value can make an apparent connection disappear!

The next goal is to optimise the mean first passage time, by building a larger database that has more direct connections between the starting and ending minima. In pathdata, COMMENT DIJINITCONTFLY 0 and add SHORTCUT <n>, where n is perhaps a quarter of the path length, or less if the path is huge. Using DUMMYRUN in pathdata can help in setting the value for <n> because a list of pairs to connect will be created etc. but no actual OPTIM jobs will be submitted. Setting too large or too small <n> will be inefficient with respect to improving the rate constants. To begin with one rate constant is likely to be much smaller than the other one. You want to optimise the rate constant as far as possible, by keeping track of the rate constants as function of the number of minima in the databases. Eventually additions of new connections to the database will no longer reduce the rate constant.