Reaction only
Perform reactions on precomputed Trajectory
You might want to apply a KIMMDY reaction to an already existing simulation. Here are some important points for doing so.
KIMMDY yaml
If you want to start your sequence of tasks with a reaction, you have to give KIMMDY a trajectory. This, you do with the trr key in the kimmdy.yml file.
Pre-averaged plumed input
Sometimes it is handy to pre-compute the averages of the distances plumed recordes. Usually, the plumed output (distances.dat) contains one line per timestep, each line starting with the time.
If you calculate the averages yourself, you end up having only one line, but need to tell KIMMDY how long the timeframe was, which was averaged. To do this, make sure to write the duration of your averaged simulation in the time field like this for a 10ps simulation:
#! FIELDS time d0 d1 d2 d3 d4
10.000000 0.142401 0.151588 0.143725 0.156734 0.152581You still need the plumed config file, even if KIMMDY does not execute plumed in the current example, as KIMMDY reads the filename of the plumed output from the plumed config.