CYANA Command: minimize - Revision history

Admin: /* Description */

2009-08-18T14:55:11Z

Description

← Older revision		Revision as of 16:55, 18 August 2009
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	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.		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 [[CYANA Macro: vtfmin\|'''vtfmin''']]:		If the information level is '''normal''' or higher, one line of information will be printed as in the following example from the macro [[CYANA Macro: vtfmin\|'''vtfmin''']]:

Admin: /* See also */

2009-08-18T14:54:24Z

Admin: /* Description */

2009-08-18T14:53:50Z

Description

← Older revision		Revision as of 16:53, 18 August 2009
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	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.		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''':		If the information level is '''normal''' or higher, one line of information will be printed out as in the following example from the macro [[CYANA Macro: vtfmin\|'''vtfmin''']]:

Admin: /* Description */

2009-08-18T14:45:54Z

Description

← Older revision		Revision as of 16:45, 18 August 2009
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	; flat: The target function was minimized by less than 1% during the preceding ''flat'' iterations.		; 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.		; 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.		Normal stop criteria are '''gradtl''', '''maxit''', and '''flat'''. Others should occur only rarely.

Admin: /* Description */

2009-08-18T14:45:40Z

Description

← Older revision		Revision as of 16:45, 18 August 2009
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	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 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:		The following stop codes may occur:
	:; ~~'''~~gradtl~~'''~~ : The squared norm of the gradient of the target function is small.		; 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.		; 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.		; 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.		; nostep: The step size during line minimization became too small.
	:; ~~'''~~uphill~~'''~~ : The direction of a conjugate gradient minimization step was uphill.		; uphill: The direction of a conjugate gradient minimization step was uphill.
	:; ~~'''~~const~~'''~~ : Several conjugate gradient steps did not succeed in decreasing the target function.		; 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.		; 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.		; stuck: Several attempts to restart the conjugate minimizer after an update of the steric interaction pair list failed.

Masayo: /* Description */

2009-08-06T15:54:50Z

Description

← Older revision		Revision as of 17:54, 6 August 2009
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	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 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:		The following stop codes may occur:
	gradtl The squared norm of the gradient of the target function is small.		:; '''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.		:; '''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.		:; '''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.		:; '''nostep''' : The step size during line minimization became too small.
	uphill The direction of a conjugate gradient minimization step was uphill.		:; '''uphill''' : The direction of a conjugate gradient minimization step was uphill.
	const Several conjugate gradient steps did not succeed in decreasing the target function.		:; '''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.		:; '''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.		:; '''stuck''' : Several attempts to restart the conjugate minimizer after an update of the steric interaction pair list failed.

Masayo: /* Description */

2009-08-06T15:47:04Z

Description

@@ Line 10: / Line 10: @@
 == 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''':
    Minimization (standard strategy):
@@ Line 38: / Line 23: @@
   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.
 The following stop codes may occur:
-Normal stop criteria are '''gradtl''', '''maxit''', and '''flat'''. Others should
+Normal stop criteria are '''gradtl''', '''maxit''', and '''flat'''. Others should occur only rarely.
 == See also ==
 * [[vtfmin]]

Admin: 1 revision

2009-01-29T11:26:56Z

1 revision

New page

== 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]]

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

	* [[vtfmin]]		* [[CYANA Macro: vtfmin\|'''vtfmin''']]