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This Mover reports a probability distribution of amino acids for a given set of positions, depending on your TaskOperations and input files. The values are reported to the log file and dumped as a set of transfacs.

<GenMeanFieldMover name="&string" threshold="(10.0 &float)" lambda_memory="(0.5 &float)" tolerance="(0.0001 &float)" temperature="(0.8 &float)" task_operations="(&string,&string,&string)" />
  • threshold: The threshold to use for truncation of energies in the Boltzmann weighting scheme. Truncation is required so as not to end up with nan values. A value of 5 is the current best-tested value.

  • lambda_memory: Prevents oscillation of the mean-field iteration and increases speed of convergence. A value of 0.5 is the current best-tested value.

  • tolerance: At what point convergence is considered reached.

  • temperature: kT for the Boltzmann weighting. A value of 0.8 is the current best-tested value.

  • task_operations: Comma separated list of task operations. Amino acid probability distributions are generated for all designed positions.

Command-line accessible options

  • bb_list: file that contains list of pdbs to run MF on, in the flexible backbone use case.
  • dump_transfac: path to location at which to dump transfac probability distribution files.

See Also