wham_analysis
wham_analysis can compute a free energy curve/surface along certain reaction coordinate(s). This utility supports two types of input; (1) trajectory (dcdfile) or (2) collective variable (cvfile). Basically, we recommend you to use the latter style, since that overall computational cost is usually lower than the former one. You should prepare cvfile from trj_analysis or something equivalent to it at first. We here show sample input files of wham_analysis. (One-dimensional sample is almost the same as the one used in Tutorial-2.2.) Note that this wham_analysis supports OpenMP parallelization. If you can use a multicore CPU in this analysis, setting OMP_NUM_THREADS environmental variable may improve the efficiency of wham calculations.
# Sample of one-dimensional wham [INPUT] cvfile = input{}.cv # Collective variable file # For REUS runs, # list of values for each replica parameter ID # (you may need to run remd_convert or something # equivalent to prepare input data) [OUTPUT] pmffile = output.pmf # potential of mean force file [WHAM] dimension = 1 # WHAM dimension nblocks = 1 # number of data blocks (>0) # input data will be evenly divided into nblocks # blocks solved independently and then merged # if you have too many amounts of data, # you may consider to increase this value temperature = 300.0 # temperature used for pmf calculation (K) tolerance = 10E-08 # convergence criterion rest_function1 = 1 # restraint function grids1 = 0.0 15.0 301 # grid definition # (min value) (max value) (number of grids) # in this case, grid size is 0.05. # (number of grids) might be determined as # ((max value) - (min_value) / (gridsize)) + 1 [RESTRAINTS] # function type should not be specified if cvfiles are used 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 7.32 \ 8.24 9.16 10.08 11.00 11.92 12.84 13.76 is_periodic1 = NO # (whether first and last ones are adjacent)
# Sample of two-dimensional wham [INPUT] cvfile = cv{}.dat # 1D series. if there are 2*4 replicas, # cv1.dat .. cv8.dat will be used. [OUTPUT] pmffile = pmf.dat [WHAM] dimension = 2 # 3 or more higher dimensions are not yet supported nblocks = 1 # nblocks > 1 is not supported for 2d temperature = 300 tolerance = 1E-08 rest_function1 = 1 rest_function2 = 2 grids2 = 4.0 11.0 71 grids1 = 7.0 15.0 81 [RESTRAINTS] constant2 = 3.0 3.0 3.0 3.0 3.0 3.0 3.0 reference2 = 5.5 6.5 7.2 7.9 8.7 9.5 10.3 is_periodic2 = NO constant1 = 2.0 2.0 2.0 2.0 2.0 2.0 reference1 = 7.5 8.75 9.5 10.5 11.5 12.5 is_periodic1 = NO
cvfile format:
(step) (value1) (value2) ....
Number of values must be the same as “dimension” parameter value in [WHAM] section. Step numbers (1st column) are required but not used in the actual calculations.
Example cvfile (intermediate data of Tutorial-2.2): steps and distances of replica parameter 1 (calculated by trj_analysis)
1 2.088 2 2.300 3 1.810 4 2.324 5 2.522 6 2.585 7 2.117 8 2.356 9 2.185 10 2.048 ...
Example cvfile (2D):
100 7.6504 4.9960 200 7.7205 4.9158 300 7.7520 5.0611 400 7.7510 4.9667 500 7.7095 5.1865 600 7.6802 4.9187 700 7.6914 5.0818 800 7.7069 5.3156 900 7.6633 5.4473 1000 7.6438 4.9710 ...