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	<id>https://cyana.org/w/index.php?action=history&amp;feed=atom&amp;title=Minimize</id>
	<title>Minimize - Revision history</title>
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	<updated>2026-04-20T03:59:14Z</updated>
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	<entry>
		<id>https://cyana.org/w/index.php?title=Minimize&amp;diff=3769&amp;oldid=prev</id>
		<title>Admin: 1 revision</title>
		<link rel="alternate" type="text/html" href="https://cyana.org/w/index.php?title=Minimize&amp;diff=3769&amp;oldid=prev"/>
		<updated>2009-01-28T18:18:39Z</updated>

		<summary type="html">&lt;p&gt;1 revision&lt;/p&gt;
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				&lt;td colspan=&quot;1&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 20:18, 28 January 2009&lt;/td&gt;
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		<author><name>Admin</name></author>
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		<id>https://cyana.org/w/index.php?title=Minimize&amp;diff=2967&amp;oldid=prev</id>
		<title>Admin: 1 revision</title>
		<link rel="alternate" type="text/html" href="https://cyana.org/w/index.php?title=Minimize&amp;diff=2967&amp;oldid=prev"/>
		<updated>2009-01-28T18:12:27Z</updated>

		<summary type="html">&lt;p&gt;1 revision&lt;/p&gt;
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&lt;tr&gt;&lt;td class=&quot;diff-marker&quot; data-marker=&quot;−&quot;&gt;&lt;/td&gt;&lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt; &lt;/div&gt;&lt;/td&gt;&lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;&lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;= minimize =&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-side-deleted&quot;&gt;&lt;/td&gt;&lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;&lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;      &lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Parameters ==&lt;/div&gt;&lt;/td&gt;&lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Parameters ==&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
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&lt;/table&gt;</summary>
		<author><name>Admin</name></author>
	</entry>
	<entry>
		<id>https://cyana.org/w/index.php?title=Minimize&amp;diff=2155&amp;oldid=prev</id>
		<title>Admin: 1 revision</title>
		<link rel="alternate" type="text/html" href="https://cyana.org/w/index.php?title=Minimize&amp;diff=2155&amp;oldid=prev"/>
		<updated>2009-01-28T17:25:56Z</updated>

		<summary type="html">&lt;p&gt;1 revision&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;&lt;br /&gt;
== Parameters ==&lt;br /&gt;
&lt;br /&gt;
; steps=&amp;#039;&amp;#039;integer&amp;#039;&amp;#039;: (default: 100)&lt;br /&gt;
; level=&amp;#039;&amp;#039;integer&amp;#039;&amp;#039;: (default: 0)&lt;br /&gt;
; flat=&amp;#039;&amp;#039;integer&amp;#039;&amp;#039;: (default: 100)&lt;br /&gt;
; angdev=&amp;#039;&amp;#039;real&amp;#039;&amp;#039;: (default: 10.0)&lt;br /&gt;
; vdwupdate=&amp;#039;&amp;#039;integer&amp;#039;&amp;#039;: (default: 100)&lt;br /&gt;
&lt;br /&gt;
== Description ==&lt;br /&gt;
&lt;br /&gt;
This command performs conjugate gradient minimization of the current&lt;br /&gt;
structure with the following parameters:&lt;br /&gt;
&lt;br /&gt;
  steps        maximal number of minimization steps (target function&lt;br /&gt;
               evaluations)&lt;br /&gt;
  level        maximal residue index difference for restraints&lt;br /&gt;
               that are included into the target function&lt;br /&gt;
  flat         the minimization is stopped if the target function&lt;br /&gt;
               did not decrease by at least 1% in the given number&lt;br /&gt;
               of steps&lt;br /&gt;
  angdev       maximal change of a dihedral angle (in degrees)&lt;br /&gt;
               between two updates of the van der Waals pair list&lt;br /&gt;
  vdwupdate    maximal number of minimization steps between two&lt;br /&gt;
               updates of the van der Waals pair list&lt;br /&gt;
&lt;br /&gt;
If the information level is normal or higher, one line of information&lt;br /&gt;
will be printed out as in the following example from the macro&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;vtfmin&amp;#039;&amp;#039;&amp;#039;:&lt;br /&gt;
&lt;br /&gt;
  Minimization (standard strategy):&lt;br /&gt;
   lev    upper    lower        vdw   angle target funct. |grad| #up #f stop&lt;br /&gt;
          # act    # act     #  act   # act  begin    end    end&lt;br /&gt;
     0  115  13    0   0   313   26  84   9 282.65   0.13 1.8E-2   0 150 maxit&lt;br /&gt;
     1  271  47    0   0   925   73  84   5 163.09   3.79   0.16  34 150 maxit&lt;br /&gt;
     2  299  51    0   0  1067   81  84   5  24.71   3.79   0.11  18 150 maxit&lt;br /&gt;
     3  381  57    0   0  1240   92  84   8 694.27   4.22   0.27  20 116 flat&lt;br /&gt;
     4  431  74    0   0  1335   90  84  10  21.83   4.47   0.16   9 130 flat&lt;br /&gt;
&lt;br /&gt;
The first column gives the minimization level. Then, there are four&lt;br /&gt;
times two columns giving the total number of restraints and the number&lt;br /&gt;
of &amp;quot;active&amp;quot; restraints for the upper limit restraints, the lower&lt;br /&gt;
limit restraints, the intrinsic van der Waals lower limit restraints,&lt;br /&gt;
and the angle restraints, respectively. &amp;quot;Active&amp;quot; restraints are those&lt;br /&gt;
that yield non-vanishing (but often small) contributions to the target&lt;br /&gt;
function. The next columns give the value of the target function at&lt;br /&gt;
the beginning and at the end of the minimization step, the norm of the&lt;br /&gt;
gradient of the target function at the end of the minimization step,&lt;br /&gt;
the number of updates of the van der Waals contact list, the number&lt;br /&gt;
of target function evaluations, and a stop code.&lt;br /&gt;
&lt;br /&gt;
The following stop codes may occur:&lt;br /&gt;
&lt;br /&gt;
  gradtl  The squared norm of the gradient of the target&lt;br /&gt;
          function is smaller than the value of the parameter&lt;br /&gt;
          GSQTOL in the subroutine CGMIN.&lt;br /&gt;
  maxit   The maximal number of target function evaluations,&lt;br /&gt;
          given by the parameter &amp;#039;&amp;#039;&amp;#039;steps&amp;#039;&amp;#039;&amp;#039;, has been exceeded.&lt;br /&gt;
  linmin  The maximal number of target function evaluations&lt;br /&gt;
          during the one-dimensional line minimization was&lt;br /&gt;
          exceeded without decreasing the target function.&lt;br /&gt;
  nostep  The step size during line minimization became too small.&lt;br /&gt;
  uphill  The direction of a conjugate gradient minimization&lt;br /&gt;
          step was uphill.&lt;br /&gt;
  const   Several conjugate gradient steps did not succeed in&lt;br /&gt;
          decreasing the target function.&lt;br /&gt;
  flat    The target function was minimized by less than 1%&lt;br /&gt;
          during the preceding &amp;#039;&amp;#039;flat&amp;#039;&amp;#039; minimization steps.&lt;br /&gt;
  stuck   Several attempts to restart the conjugate minimizer&lt;br /&gt;
          after an update of the steric interaction pair list&lt;br /&gt;
          failed.&lt;br /&gt;
&lt;br /&gt;
Normal stop criteria are &amp;#039;&amp;#039;&amp;#039;gradtl&amp;#039;&amp;#039;&amp;#039;, &amp;#039;&amp;#039;&amp;#039;maxit&amp;#039;&amp;#039;&amp;#039;, and &amp;#039;&amp;#039;&amp;#039;flat&amp;#039;&amp;#039;&amp;#039;. Others should&lt;br /&gt;
occur only rarely.&lt;br /&gt;
&lt;br /&gt;
== See also ==&lt;br /&gt;
&lt;br /&gt;
* [[vtfmin]]&lt;/div&gt;</summary>
		<author><name>Admin</name></author>
	</entry>
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