PROFASI  Version 1.5
Commands for setting up measurements/Observables

If the simulation is to make a certain measurement during the run, there are two things one has to do: 1. One has to tell the simulation program what that measurement is. 2. One might want to (have to) fine-tune the measurement with some additional information.

When multiple options are passed to an Observable, either with new_obs or with set_obs, they should be separated by semi-colon (";") marks. There need not be a semi-colon after the last option. For example, the following adds a backbone RMSD measurement between residues 20 – 30 in a PDB file and the corresponding residues in the simulation: –new_obs ProteinRMSD bbrmsd "using +BB+CB ; struc1 abc.pdb::A,20,30 ; struc2: $::A"

Available Observables in PROFASI

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2