Rst-wham: Difference between revisions
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|<span style="color: blue;">metadata</span><br/><span style="margin-left: 30px;">Each line of the metadata file should be blank, begin with a "#" (marking a comment), or have the following format: | |<span style="color: blue;">metadata</span><br/><span style="margin-left: 30px;">Each line of the metadata file should be blank, begin with a "#" (marking a comment), or have the following format: | ||
<code>/path/to/timeseries/file loc_win_min spring [correl time] [temperature]</code> | ::<code>/path/to/timeseries/file loc_win_min spring [correl time] [temperature]</code> | ||
This first field is the name of one of the time series files (more on this in a moment). The second field, loc_win_min, is the location of the minimum of the biasing potential for this simulation, a floating point number. The third field, spring, is the spring constant for the biasing potential used in this simulation, assuming the biasing potential is of the format | {{Outdent|:}}This first field is the name of one of the time series files (more on this in a moment). The second field, loc_win_min, is the location of the minimum of the biasing potential for this simulation, a floating point number. The third field, spring, is the spring constant for the biasing potential used in this simulation, assuming the biasing potential is of the format | ||
{{Outdent|:}}Many simulation packages, including TINKER, AMBER, and CHARMM, do not include the [1/2] when they specify spring constants for their restraint terms. This is a common source of error (I'd love to change my code to match the other packages' behavior, but then experienced users who don't read the manual would get messed up). Also, the units for the spring constant must match those for the time series. So, if your time series is a distance recorded in Ångstroms, the spring constant must be in kcal/mol-Å2. AMBER users should take care when using angular restraints: the specification and output of angles is in degrees, but AMBER's spring constants use kcal/mol-rad2. | |||
The fourth argument ("correl time") specifies the decorrelation time for your time series, in units of time steps. It is only used when generating fake data sets for Monte Carlo bootstrap error analysis, where it modulates the number of points per fake data set. This argument is optional, and is ignored if you don't do error analysis. If you're doing multiple temperatures but not bootstrapping, set it to any integer value as a placeholder, and it'll be ignored. See section for more discussion about how to do bootstrapping. | |||
Finally, the last (optional) field is the temperature for this simulation. If not supplied, the temperature specified on the command line is used. In the present version of the code, you must either leave the temperature unspecified for all simulations or specify it for all simulations. | |||
The time series files must follow one of two formats, depending on whether the temperature was specified in the metadata file. If no temperature was specified, the file should contain two columns, where the first is the time (which isn't actually used), and the second is the position of the system along the reaction coordinate. Both numbers should be in floating point format. Lines beginning with "#" are ignored as comments. Additional columns of data are ignored. | |||
If the simulation temperature is specified, there must be a third column of data, containing the system's potential energy at that time point. It should be a floating point value. | |||
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