mbar_analysis
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 [INPUT] cvfile = ../5_calc_dist/parameter/{}.dis # input cv file [OUTPUT] fenefile = fene.dat # relative free energy between windows pmffile = pmf.dat # potential of mean force weightfile = {}.weight # sample weights used by pmf_analysis [MBAR] 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 [RESTRAINTS] 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