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File formats

As with regular 1 dimensional wham, each line of the metadata file should either be blank, begin with a ``#'', or have the following format

/path/to/timeseries/file loc_win_x loc_win_y spring_x spring_y [correl time] [temperature]

This first field is the name of one of the time series files. loc_win_x and loc_win_y are the locations of the minimum of the biasing terms in the first and second dimensions of the reaction coordinate. spring_x and spring_y are the spring constants used for the biasing potential in this simulation, assuming the biasing potential is of the format


\begin{displaymath}
V = \frac{1}{2} ( k_x * (x - x_0)^2 + k_y * (y -y_0)^2 )
\end{displaymath} (2)

The sixth 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 5.2 for more discussion about how to do bootstrapping.

Finally, the last field is the temperature this simulation was run at. 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 three columns, where the first is the time (which isn't actually used), and the second and third are the position of the system along the x and y reaction coordinates, respectively. 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 fourth column of data, containing the system's potential energy at that time point. It should be a floating point value. See the section on replica exchange for more details.


next up previous contents
Next: Output Up: wham-2d Previous: Command line arguments   Contents
Alan Grossfield 2007-11-13