Rst-wham: Difference between revisions
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'''Synopsis''' | '''Synopsis''' | ||
<span style="color: maroon;"></span> <span style="color: blue;"></span> <span style="color: purple;"> | <span style="color: maroon;">wham</span> <span style="color: blue;">[P|Ppi|Pval] </span> <span style="color: purple;">hist_min hist_max num_bins tol temperature numpad metadatafile freefile </span><span style="color: blue;">[num_MC_trials randSeed] </span> | ||
'''Description''' | '''Description''' | ||
These programs (wham and wham-2d) implement the Weighted Histogram Analysis Method of Kumar, et al ("Multidimensional free-energy calculations using the weighted histogram analysis method", J. Comput. Chem., 16:1339-1350, 1995). The code generally follows the notation used by Benoit Roux ("The calculation of the potential of mean force using computer simulations", Comput. Phys. Comm., 91:275-282, 1995). Consult these papers for the theoretical background and justification for the method. | |||
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|- style="vertical-align: top; background-color: #e6e6e6;" | |||
| <span style="color: purple;">hist_min hist_max</span><br/> | |||
<span style="margin-left: 30px;">Specify the boundaries of the histogram. As a rule, all data points outside the range (hist_min, hist_max) are silently ignored. The only exception is that if an entire trajectory is outside the range, the program halts with an error message. The solution is to remove that file from the metadata file. hist_min and hist_max should be floating point numbers. </span> | |||
|- style="vertical-align: top;" | |||
| <span style="color: purple;">num_bins</span><br/> | |||
<span style="margin-left: 30px;">Specifies the number of bins in the histogram, and as a result the number of points in the final PMF. It should be an integer.</span> | |||
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Revision as of 14:00, 18 April 2016
Navigation: Documentation / Methods / Restrained Dynamics / RST:Utilities / rst-wham
RST Utilities
Name
rst-wham
Synopsis
wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]
Description These programs (wham and wham-2d) implement the Weighted Histogram Analysis Method of Kumar, et al ("Multidimensional free-energy calculations using the weighted histogram analysis method", J. Comput. Chem., 16:1339-1350, 1995). The code generally follows the notation used by Benoit Roux ("The calculation of the potential of mean force using computer simulations", Comput. Phys. Comm., 91:275-282, 1995). Consult these papers for the theoretical background and justification for the method.
Arguments
| hist_min hist_max Specify the boundaries of the histogram. As a rule, all data points outside the range (hist_min, hist_max) are silently ignored. The only exception is that if an entire trajectory is outside the range, the program halts with an error message. The solution is to remove that file from the metadata file. hist_min and hist_max should be floating point numbers. |
| num_bins Specifies the number of bins in the histogram, and as a result the number of points in the final PMF. It should be an integer.
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Options