Hello Yuan-- > > I have been trying but I cannot find the way to modify the time step for the > simulated annealing. Is it controlled by the "stepsize" parameter? How do I > define it in the python script?
you can set the initial step size using the stepsize argument to protocol.initDynamics. However, by default this stepsize is adjusted to conserve energy to within the IVM property eTolerance. If you would instead like to use constant timestep size, you will have to call the IVM accessor adjustStepsize(False) after configuration with initDynamics. > > On a remote subject, I wonder if there is a guidance on how to systematically > optimize the force constants used for different types of restraints (noe, > dihedrals, hbonds, pcs, rdc, etc.). I would start with the example script (in eginput) and adjust values, if necessary, i.e. if an observable is not fit to within the expected tolerance. I hope this helps-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
