pmf_analysis utility calculates the potential of mean force (or free energy profile) along given collective variable (CV) coordinates. This utility can be used with the outputs (weight files) of mbar_analysis and pathcv_analysis. An example shown below illustrates a 1-dimensional free energy profile calculation by using CV and weight files (output of mbar_analysis). Tutorial of the string method and its material also illustrates a usage of this utility.

cvfile       = {}.cv          # Collective variable files
weightfile   = {}.weight      # weight files from mbar_analysis
pmffile      = output.pmf     # potential of mean force file
nreplica     = 16             # number of replicas
dimension    = 1              # dimension of cv space
temperature  = 300            # temperature (K)
grids1       = 1.0 360.0 360    # (min max num_of_bins)
band_width1  = 0.1            # sigma of gaussian kernel
is_periodic1 = YES            # periodicity of cv1
box_size1    = 360.0          # periodic range of cv1

The input cvfiles can be different from those used in mbar_analysis. This means you can “transform” the pmf onto some other cv space. For example, you can calculate the free energy profie along a dihedral angle from REUS using a atomic distance coordinates, by following the procedure described below,

  1. perform REUS run using a distance as CV
  2. analyze pmf using mbar_analysis (free energy along the distance)
  3. using the weight files from 2, run pmf_analysis using a dihedral angle as CV (free energy along the dihedral angle)

Please check mbar_analysis page for weight files.