The analysis Stage

Analysis
  • Overview
  • Default Configuration

Keywords for the analysis stage are listed in Table 1

Table 1. Keywords for the analysis stage

Keywords

Description

meta.range

For metadynamics simulations, specify the range for each collective variable, in the format [[min1 max1] [min2 max2] ... ].

meta.nbin

For metadynamics simulations, specify the number of bins for each collective variable in the analysis.

plotter

Specify the plotter to use to draw images for figures. Allowed values: mplchart, gchart. mplchart generates static .png file for each figure. 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.

prob_profile

Specify how to calculate the probability profiles for the time series given by the time_series parameter. Example: prob_profile = [2 0 360 true], which means the bin size is 2, the data range is [0, 360), and the range is periodic (true).

report

Specify the name of the report file. Default: $JOBNAME_report.html.

SEA

Block for specifying the configuration of the simulation event analysis. This block can be the contents of an .st2 file.

time_series

Specify the variables for which to analyze the time series. Example: time_series = [[dihedral 1 2 3 4] [dihedral 5 6 7 8]], which specifies two dihedral angles to analyze.

Default configurations for the analysis stage. A {type} value is shown for keywords which do not have defaults set. See General multisim Stage Keywords for descriptions of general keywords

{
   SEA = false
   compress = "$MAINJOBNAME_$STAGENO-out.tgz"
   dir = "$[$JOBPREFIX/$]$[$PREFIX/$]$MAINJOBNAME_$STAGENO"
   dryrun = false
   effect_if = {list}
   jlaunch_opt = []
   jobname = "$MAINJOBNAME_$STAGENO"
   meta = {
      nbin = [51 ]
      range = []
   }
   plotter = mplchart
   prefix = ""
   prob_profile = []
   report = "$MAINJOBNAME_$STAGENO_report.html"
   should_skip = false
   should_sync = true
   struct_output = ""
   time_series = []
   title = {str}
   transfer_asap = false
}