README

usage: MetaD_analysis_0.1.1.py [-h] [-n] [-cvs rg ab [rg ab ...]]
                               [-stride t [fs]] [-temp 298 [K]]
                               [-hills ./HILLS] [-colvar ./colvar]
                               [-plumed /usr/local/plumed-2.2.0/bin/plumed]
                               [-plot] [-pdf filename.pdf] [-nocolvar]
                               [-nohills] [-nt N] [-no2D]
                               [-rg | -xtc fname.xtc | -gro fname.gro]

This is a script that can assist in plotting data of MetaD simulations run with plumed2 with matplotlib. The script runs sum_hills for specified CVs and the the combination pairs of those.

Very basic command, plot + write pdf of all CVs and combinations:
python MetaD_analysis.py -plot -pdf plot.pdf -stride 20000

optional arguments:
  -h, --help            show this help message and exit
  -n                    Dry run, no sum_hills calculation. Use if calculation
                        is already run before
  -cvs rg ab [rg ab ...]
                        Specified CVs. If no CVs specified: Sumhills for all
                        CVs+pairs of those will be run.
  -stride t [fs]        Stride length
  -temp 298 [K]         Specify temperature of simulation in Kelvin
  -hills ./HILLS        Location of Hills file
  -colvar ./colvar      Location of the colvar file
  -plumed /usr/local/plumed-2.2.0/bin/plumed
                        plumed location
  -plot                 Plot in window
  -pdf filename.pdf     Write .pdf at specified file location
  -nocolvar             Do not plot the CVs from colvar
  -nohills              Do not plot the hillsheight
  -nt N                 specify number of threads
  -no2D                 Do not run 2D sum_hills
  -rg                   Plot Rg from .xtc and .gro file
  -xtc fname.xtc        specify .xtc file
  -gro fname.gro        specify .gro file

MetaD_analysis_0.1.3.py is a version where the minimum value of the free energy
is set to zero