pmf_analysis
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.
[INPUT] cvfile = {}.cv # Collective variable files weightfile = {}.weight # weight files from mbar_analysis [OUTPUT] pmffile = output.pmf # potential of mean force file [OPTION] 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,
- perform REUS run using a distance as CV
- analyze pmf using mbar_analysis (free energy along the distance)
- 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.