CYANA Command: minimize: Difference between revisions

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== Description ==
== Description ==


This command performs conjugate gradient minimization of the current
Performs conjugate gradient minimization ''steps''. Restraints up to the given minimization ''level'' are included in the target function. The conjugate gradient minimizer is stopped if within ''flat'' minimization steps the target function cannot be reduced by at least 1%.  The van der Waals interaction list is updated every ''vdwupdate'' steps or each time a torsion angle has changed its value by more than ''angedev'' degrees since the last update of the van der Waals interaction list.
structure with the following parameters:
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''':


  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):
   Minimization (standard strategy):
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     4  431  74    0  0  1335  90  84  10  21.83  4.47  0.16  9 130 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
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.
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:
The following stop codes may occur:
gradtl The squared norm of the gradient of the target function is small.
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 has been exceeded without decreasing the target function value.
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 iterations.
stuck Several attempts to restart the conjugate minimizer after an update of the steric interaction pair list failed.


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


== See also ==
== See also ==


* [[vtfmin]]
* [[vtfmin]]

Revision as of 17:47, 6 August 2009

Parameters

steps=integer
(default: 100)
level=integer
(default: 0)
flat=integer
(default: 100)
angdev=real
(default: 10.0)
vdwupdate=integer
(default: 100)

Description

Performs conjugate gradient minimization steps. Restraints up to the given minimization level are included in the target function. The conjugate gradient minimizer is stopped if within flat minimization steps the target function cannot be reduced by at least 1%. The van der Waals interaction list is updated every vdwupdate steps or each time a torsion angle has changed its value by more than angedev degrees since the last update of the van der Waals interaction 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 small. 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 has been exceeded without decreasing the target function value. 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 iterations. 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

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