Parameter Table

keyword	variable name	allowed values	default
minimize	minimize	yes no	no
simplex_iterations	sim_itmax	integer	500
simplex_convergence	sim_cnvrgE	real	0.2
simplex_restart	sim_need_to_restart	real	1.0
simplex_initial_translation	sim_trnstep	real	1.0
simplex_initial_rotation	sim_rotstep	real	0.5

Parameter Descriptions

minimize

indicates whether to perform force-field score optimization. This functionality is further described in the Force-Field Score Optimization section.

simplex_iterations

specifies the maximum number of iterations of simplex minimization to perform. Values on the order of 10 to 25 offer a crude optimization, while values on the order of 500 provide complete convergence.

simplex_convergence

provides a low-level stringency for the minimization. The upper and lower bound of the simplex must converge to within simplex_convergence kcal/mol to assess completion (see simplex_restart).

simplex_restart

provides a high-level stringency for the minimization. The convergence of each simplex (see simplex_convergence) prompts the initiation of another simplex. If the force-field score resulting from one simplex is less than that of the previous simplex by no more than simplex_restart kcal/mol, the minimization is deemed complete.

simplex_initial_translation

is the maximum step size the simplex may take (in Ångstroms) in choosing an initial direction for the translational degrees of freedom in the minimization.

simplex_initial_rotation

is the maximum step size the simplex may take (in degrees) in choosing an initial direction for the rotational degrees of freedom in the minimization.