CYANA Command: minimize

Parameters

steps=integer

(default: 100)

level=integer

(default: 0)

flat=integer

(default: 100)

angdev=real

(default: 10.0)

vdwupdate=integer

(default: 100)

Description

This command performs conjugate gradient minimization of the current structure with the following parameters:

 steps        maximal number of minimization steps (target function
              evaluations)
 level        maximal residue index difference for restraints
              that are included into the target function
 flat         the minimization is stopped if the target function
              did not decrease by at least 1% in the given number
              of steps
 angdev       maximal change of a dihedral angle (in degrees)
              between two updates of the van der Waals pair list
 vdwupdate    maximal number of minimization steps between two
              updates of the van der Waals pair list

If the information level is normal or higher, one line of information will be printed out as in the following example from the macro vtfmin:

 Minimization (standard strategy):
  lev    upper    lower        vdw   angle target funct. |grad| #up #f stop
         # act    # act     #  act   # act  begin    end    end
    0  115  13    0   0   313   26  84   9 282.65   0.13 1.8E-2   0 150 maxit
    1  271  47    0   0   925   73  84   5 163.09   3.79   0.16  34 150 maxit
    2  299  51    0   0  1067   81  84   5  24.71   3.79   0.11  18 150 maxit
    3  381  57    0   0  1240   92  84   8 694.27   4.22   0.27  20 116 flat
    4  431  74    0   0  1335   90  84  10  21.83   4.47   0.16   9 130 flat

The first column gives the minimization level. Then, there are four times two columns giving the total number of restraints and the number of "active" restraints for the upper limit restraints, the lower limit restraints, the intrinsic van der Waals lower limit restraints, and the angle restraints, respectively. "Active" restraints are those that yield non-vanishing (but often small) contributions to the target function. The next columns give the value of the target function at the beginning and at the end of the minimization step, the norm of the gradient of the target function at the end of the minimization step, the number of updates of the van der Waals contact list, the number of target function evaluations, and a stop code.

The following stop codes may occur:

 gradtl  The squared norm of the gradient of the target
         function is smaller than the value of the parameter
         GSQTOL in the subroutine CGMIN.
 maxit   The maximal number of target function evaluations,
         given by the parameter steps, has been exceeded.
 linmin  The maximal number of target function evaluations
         during the one-dimensional line minimization was
         exceeded without decreasing the target function.
 nostep  The step size during line minimization became too small.
 uphill  The direction of a conjugate gradient minimization
         step was uphill.
 const   Several conjugate gradient steps did not succeed in
         decreasing the target function.
 flat    The target function was minimized by less than 1%
         during the preceding flat minimization steps.
 stuck   Several attempts to restart the conjugate minimizer
         after an update of the steric interaction pair list
         failed.

Normal stop criteria are gradtl, maxit, and flat. Others should occur only rarely.

See also

• vtfmin