The fep_analysis Stage

Keywords for the fep_analysis stage are listed in Table 1.

Table 1. Keywords for the fep_analysis stage

Keywords	Description
bennett.random_seed	Random seed for the Bennett method. Default: 2111839.
correct_vdw	Calculate the long range dispersion correction for absolute free energy jobs. This keyword has no effect for relative free energy jobs. Default: true.
correct_restr	Calculate the enthalpic correction for position restraints. This parameter does no harm if the production simulations have no restraints. Default: true.
plotter	Specify the plotter to use to draw images for figures. Allowed values: mplchart, gchart. mplchart generates static .png file for each figure. Choosing gchart generates a URL for each figure, and the URLs are saved in the report file. When you open the report file in a browser, the figure images are generated using Google chart APIs. The data for the figures is sent to the Google web site to create the images. Default: mplchart.
report	Specify the name of the report file. Default: $JOBNAME_report.html.

The free energy can be plotted as different functions of the simulation time. The following settings are added to control these new functionalities:

    bennett = {
       forward_time = {
          name  = "freeenergy_time"
          begin = 100.0
          end   = inf
          dt    = 30.0
       }
       reversed_time = {
          name  = "freeenergy_rtime"
          begin = 100.0
          end   = inf
          dt    = 30.0
       }
       sliding_time = {
          name   = "freeenergy_stime"
          begin  = 100.0
          end    = inf
          dt     = 30.0
          window = 500.0
       }
    }

The forward_time, reversed_time, and sliding_time settings control calculations of the free energy over different ranges of time.

The forward_time keyword provides the free energy as a function of the simulation course. In other words, each free energy value of this function is calculated using the trajectory fragment from the time as given by the begin setting to the time point. The dt keyword indicates the interval between consecutive estimates of the free energy (in this case, 30 ps).

The reversed_time keyword functions similarly to the forward_time keyword except that the free energy is calculated from each time point to the end of the trajectory.

For the sliding_time keyword, the fragment length has a fixed length, specified by the window keyword (in this case, 500.0 ps). The beginning of the fragment slides along the trajectory with the step size given by the dt keyword (30.0 ps in this example).

{
   bennett = {
      _override_temperature = 0.0
      forward_time = {
         begin = 100.0
         dt = "150:points"
         end = inf
         name = freeenergy_time
      }
      random_seed = 2111839
      reversed_time = {
         begin = 100.0
         dt = "150:points"
         end = inf
         name = freeenergy_rtime
      }
      sliding_time = {
         begin = 100.0
         dt = "150:points"
         end = inf
         name = freeenergy_stime
         window = 500.0
      }
   }
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   correct_coul = false
   correct_restr = true
   correct_vdw = false
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   dryrun = false
   effect_if = {list}
   fep_type = small_molecule
   include_sid = true
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   plotter = mplchart
   prefix = ""
   report = "$JOBNAME.html"
   should_skip = false
   should_sync = true
   struct_output = ""
   title = {str}
   transfer_asap = false
}