Energy minimization used (1) 106 steps of energy minimization, (2) a dielectric multiplicative constant of 80.0, (3) the steepest descent or conjugate gradient method, (4) a nonbonded cut-off of 12 Å, (9) a 10−7-kcal/(moleÅ) cut-off for the root-mean-square of the Cartesian elements of the gradient, and (10) defaults for other inputs of the SANDER module.
Energy minimization used (1) 106 steps of energy minimization, (2) a dielectric multiplicative constant of 80.0, (3) the steepest descent or conjugate gradient method, (4) a nonbonded cut-off of 12 Å, (9) a 10−7-kcal/(moleÅ) cut-off for the root-mean-square of the Cartesian elements of the gradient, and (10) defaults for other inputs of the SANDER module of the AMBER 5 program [28].
A constrained minimization using few steps of steepest descent method was carried out to insure the removal of any close bad contacts among the peptide atoms.
Cao et al implements L1 norm minimization by use of an expectation maximization algorithm for a linearized DOT inverse problem, and show that the reconstructed region with abnormal optical properties are localized more than the other methods they use [ 16].
Two older studies analyzed cost minimization in use of malaria chemoprophylaxis in travellers and concluded that malaria chemoprophylaxis is cost-effective from the perspective from the British health care system and also from the German and Swiss systems respectively [ 25, 26].
It then uses the minimization function of MATLAB (MathWorks, Natick, MA) to further refine the channel distribution.
With water molecules stripped off, the average structure with the shortest distance was then energy minimized (performing 50 cycles of steepest-descent minimization and then 150 cycles of conjugate-gradient minimization using a dielectric constant of 80.0).
The least square minimization, using larger number of CFD samples, is recommended for current test cases.
The energy minimization used the default method of AMBER 5.0 (10 cycles of the steepest descent method followed by the conjugate gradient method).
The complex was refined by energy minimization using a dielectric constant of 1.0 and 100 cycles of steepest-descent minimization followed by 100 cycles of conjugate-gradient minimization.
