Multistate Bennett acceptance ratio (MBAR; JCP 129, 124105 (2008)) method estimates relative free energy between states. Using this method, mbar_analysis utility calculates relative free energies from given data sets. MBAR is a kind of general purpose method and the method is applicable to various kinds of calculations (such as free energy surface, binding free energy, etc.). Currently, mbar_analysis of GENESIS is able to treat the data sets of umbrella sampling, temperature-REMD, REST, FEP, and REST.

As like wham_analysis, mbar_analysis supports two types of input files, (1) trajectory files (dcdfile) and (2) collective variable files (cvfile).  cvfile file, is recommended as in the case of wham_analysis. The sample below show an example of reading a cvfile. The file format of cvfile is the same as the case of wham_analysis.

Below is a sample input (ctrl) file for mbar_analysis. This input calculates the relative free energy between states (the “state” here means a umbrella window) and the free energy along the given restraint coordinate. If you would like to get the potential of mean force along a certain pathway, pathcv_analysis and pmf_analysis must be executed before using mbar_analysis. Please check samples of these utilities and string method tutorial.

mbar_analysis also supports OpenMP parallelization when the environmental variable OMP_NUM_THREADS is correctly set.

# mbar_analysis sample, keywords are almost same as that of wham_analysis
# inputs of 2D-MBAR is similar to that of 2D-wham_analysis
cvfile = ../5_calc_dist/parameter/{}.dis # input cv file

fenefile       = fene.dat     # relative free energy between windows
pmffile        = pmf.dat  # potential of mean force
weightfile     = {}.weight # sample weights used by pmf_analysis

nreplica       = 16
input_stype    = US # US REMD FEP REST MBGO
dimension      = 1
nblocks        = 1
temperature    = 300.0
target_temperature = 300.0
tolerance      = 10E-08
rest_function1 = 1
grids1         = 0.0 15.0 301

constant1      = 1.2 1.2 1.2 1.2 1.2 1.2 1.2 \
                 1.2 1.2 1.2 1.2 1.2 1.2 1.2
reference1     = 1.80 2.72 3.64 4.56 5.48 6.40 7.3 \
                 8.24 9.16 10.08 11.00 11.92 12.84 13.76
is_periodic1   = NO