GMIN - Revision history

import>Cjf41: /* #-F */

2013-09-20T11:20:45Z

#-F

← Older revision		Revision as of 11:20, 20 September 2013
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	* [[FRAUSI]]: specifies a particular tight-binding potential for silicon. See also keyword [[ANGSTROM]].		* [[FRAUSI]]: specifies a particular tight-binding potential for silicon. See also keyword [[ANGSTROM]].

	* [[FREEZE]] ''n1 n2'' <math>\ldots</math>: freeze the coordinates of atoms ''n1, n2,''<math>\ldots</math>}. Note that all the ''FREEZE'' keywords do '''NOT''' function when using [[AMBERMDSTEPS]].		* [[FREEZE]] ''n1 n2'' <math>\ldots</math>: freeze the coordinates of atoms ''n1, n2,''<math>\ldots</math>}. Note that all the ''FREEZE'' keywords do '''NOT''' function when using [[AMBERMDSTEPS]]. Use multiple FREEZE statements for larger numbers of atoms.

	* [[FREEZERES]] ''n1 n2'' <math>\ldots</math>: freeze the coordinates of all atoms in residues ''n1, n2,''<math>\ldots</math>.		* [[FREEZERES]] ''n1 n2'' <math>\ldots</math>: freeze the coordinates of all atoms in residues ''n1, n2,''<math>\ldots</math>.

import>Dw34: /* #-F */

2010-07-28T10:29:19Z

#-F

← Older revision		Revision as of 10:29, 28 July 2010
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	* [[AMCHPMIN]]: The minimum probability for a single angle to be twisted in an AMBER dihedral step.		* [[AMCHPMIN]]: The minimum probability for a single angle to be twisted in an AMBER dihedral step.

	* [[ANGSTROM]]: specifies coordinates in <math>\AA</math>ngstrom for the [[FRAUSI]] potential.		* [[ANGSTROM]]: specifies coordinates in <math>{\rm \AA}</math>ngstrom for the [[FRAUSI]] potential.

	* [[ARGON]]: introduces a diatomics-in-molecules calculation for a neutral, cationic or electronically excited argon cluster. See also [[GROUND]], [[PLUS]], [[TWOPLUS]] and [[STAR]].		* [[ARGON]]: introduces a diatomics-in-molecules calculation for a neutral, cationic or electronically excited argon cluster. See also [[GROUND]], [[PLUS]], [[TWOPLUS]] and [[STAR]].

import>Csw34: /* Keywords */

2010-07-27T09:51:24Z

Keywords

← Older revision		Revision as of 09:51, 27 July 2010
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	=== AMBER9 keywords ===		=== AMBER9 keywords ===
	=== CHARMM keywords ===		=== CHARMM keywords ===
		⚫	=== AMH keywords ===

	'''Feedback needed!'''--[[User:Csw34\|Csw34]] 09:51, 27 July 2010 (UTC)		'''Feedback needed!'''--[[User:Csw34\|Csw34]] 09:51, 27 July 2010 (UTC)

⚫	=== AMH keywords ===
	== The data file ==		== The data file ==
	Input is keyword driven with sensible defaults in most cases. Free format may be used within each line. Blank lines are ignored.		Input is keyword driven with sensible defaults in most cases. Free format may be used within each line. Blank lines are ignored.

import>Csw34: /* Keywords */

2010-07-27T09:51:04Z

Keywords

← Older revision		Revision as of 09:51, 27 July 2010
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	= Keywords =		= Keywords =

			'''I'm still deciding how to break the keywords up - it is currently done alphabetically - but it might make sense to do it by usage i.e. keywords that work only with AMBER or CHARMM in different sections''':

			=== AMBER keywords (old implementation) ===
			=== AMBER9 keywords ===
			=== CHARMM keywords ===

			'''Feedback needed!'''--[[User:Csw34\|Csw34]] 09:51, 27 July 2010 (UTC)

			=== AMH keywords ===
	== The data file ==		== The data file ==
	Input is keyword driven with sensible defaults in most cases. Free format may be used within each line. Blank lines are ignored.		Input is keyword driven with sensible defaults in most cases. Free format may be used within each line. Blank lines are ignored.

import>Csw34: /* The data file */

2010-07-27T09:49:23Z

The data file

← Older revision		Revision as of 09:49, 27 July 2010
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	The following keywords are recognised, where n and x are integer and real data, respectively.		The following keywords are recognised, where n and x are integer and real data, respectively.

	EXAMPLES FOR SPLITTING KEYWORDS UP:






	OR

	=== AMBER keywords (old implementation) ===
	=== AMBER9 keywords ===
	=== CHARMM keywords ===
	=== AMH keywords ===

	=== #-F ===		=== #-F ===

import>Csw34 at 09:48, 27 July 2010

2010-07-27T09:48:23Z

← Older revision		Revision as of 09:48, 27 July 2010
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	EXAMPLES FOR SPLITTING KEYWORDS UP:		EXAMPLES FOR SPLITTING KEYWORDS UP:


⚫	=== A-F ===

⚫	=== G-L ===

⚫	=== M-R ===

⚫	=== S-Z ===

	OR		OR
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	=== AMH keywords ===		=== AMH keywords ===

		⚫	=== #-F ===
	* [[2D]]: enforce two-dimensional `flatland'.		* [[2D]]: enforce two-dimensional `flatland'.

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	* [[FS]] ''gatom'': specifies a Finnis-Sinclair potential using parameters from Finnis and Sinclair, ''Phil.Mag.A'', '''50''', 45 (1984) and corresponding erratum ''Phil.Mag.A'', '''53''', 161 (1986). ''gatom''=1 for V, ''gatom''=2 for Nb, ''gatom''=3 for Ta, ''gatom''=4 for Cr, ''gatom''=5 for Mo, ''gatom''=6 for W, ''gatom''=7 for Fe (original parameters), ''gatom''=8 for Fe (modified parameters in erratum). Subtoutine '''FS''' was coded by James Elliott in April 2009.		* [[FS]] ''gatom'': specifies a Finnis-Sinclair potential using parameters from Finnis and Sinclair, ''Phil.Mag.A'', '''50''', 45 (1984) and corresponding erratum ''Phil.Mag.A'', '''53''', 161 (1986). ''gatom''=1 for V, ''gatom''=2 for Nb, ''gatom''=3 for Ta, ''gatom''=4 for Cr, ''gatom''=5 for Mo, ''gatom''=6 for W, ''gatom''=7 for Fe (original parameters), ''gatom''=8 for Fe (modified parameters in erratum). Subtoutine '''FS''' was coded by James Elliott in April 2009.

		⚫	=== G-L ===
	* [[GROUND]]: when combined with keywords [[NEON]] or [[ARGON]] uses an accurate (Aziz) potential to model the ground state neutral cluster.		* [[GROUND]]: when combined with keywords [[NEON]] or [[ARGON]] uses an accurate (Aziz) potential to model the ground state neutral cluster.

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	* [[LOCALSAMPLE]] ''abthresh acthresh'': Keyword currently under construction! For three groups of atoms defined in <tt>movableatoms</tt> (A,B,C), a step is quenched when the centre of coordinates of A->B is less than ''abthresh'' AND A->C is less than ''acthresh''. If this condition is broken AFTER the quench, it is automatically rejected.		* [[LOCALSAMPLE]] ''abthresh acthresh'': Keyword currently under construction! For three groups of atoms defined in <tt>movableatoms</tt> (A,B,C), a step is quenched when the centre of coordinates of A->B is less than ''abthresh'' AND A->C is less than ''acthresh''. If this condition is broken AFTER the quench, it is automatically rejected.

		⚫	=== M-R ===
	* [[MAXBFGS]] ''max'': ''max'' is the largest permitted LBFGS step.		* [[MAXBFGS]] ''max'': ''max'' is the largest permitted LBFGS step.

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	The reference geometry must be given in xyz-format in an additional file <tt>compare</tt>. ''rmssave'' is an integer that specifies the number of lowest energy geometries and RMSD <math>\le</math> ''rmslimit'' to save. Geometries are only saved if their RMSD's are more than ''rmstol'' different. The flag ''lca'' controls whether the all-atom RMSD (''lca''=0) or the <math>C_{\alpha}</math>-RMSD (''lca''=1) is calculated. The flag ''best'' determines which structure is compared to the reference after each quench. ''best''=0 implies the current quench minimum and ''best''=1 implies the current best (lowest energy) minimum. If [[TRACKDATA]] is also specified, the RMSD calculated after each quench is produced in the file <tt>rmsd</tt> in gnuplot readable format.		The reference geometry must be given in xyz-format in an additional file <tt>compare</tt>. ''rmssave'' is an integer that specifies the number of lowest energy geometries and RMSD <math>\le</math> ''rmslimit'' to save. Geometries are only saved if their RMSD's are more than ''rmstol'' different. The flag ''lca'' controls whether the all-atom RMSD (''lca''=0) or the <math>C_{\alpha}</math>-RMSD (''lca''=1) is calculated. The flag ''best'' determines which structure is compared to the reference after each quench. ''best''=0 implies the current quench minimum and ''best''=1 implies the current best (lowest energy) minimum. If [[TRACKDATA]] is also specified, the RMSD calculated after each quench is produced in the file <tt>rmsd</tt> in gnuplot readable format.

		⚫	=== S-Z ===
	* [[SAVE]] ''nsave'': ''nsave'' is an integer that specifies the number of lowest energy geometries to save and summarise in the file <tt>lowest</tt>. Arrays are now dynamically allocated, so any positive integer can be specified.		* [[SAVE]] ''nsave'': ''nsave'' is an integer that specifies the number of lowest energy geometries to save and summarise in the file <tt>lowest</tt>. Arrays are now dynamically allocated, so any positive integer can be specified.

import>Csw34 at 08:51, 27 July 2010

2010-07-27T08:51:58Z

← Older revision		Revision as of 08:51, 27 July 2010
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	[[Image:Gmin.jpg\|thumb\|GMIN in all its glory\|300px\|right]]		[[Image:Gmin.jpg\|thumb\|GMIN in all its glory\|300px\|right]]
	GMIN page - very much under construction!		'''GMIN page - very much under construction!'''

	= Introduction =		= Introduction =

import>Csw34 at 08:51, 27 July 2010

2010-07-27T08:51:44Z

← Older revision		Revision as of 08:51, 27 July 2010
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	[[Image:~~Gmin3~~.jpg\|thumb\|GMIN in all its glory\|300px\|right]]		[[Image:Gmin.jpg\|thumb\|GMIN in all its glory\|300px\|right]]
	GMIN page - very much under construction!		GMIN page - very much under construction!

import>Csw34 at 00:54, 27 July 2010

2010-07-27T00:54:08Z

Show changes

import>Csw34 at 00:30, 27 July 2010

2010-07-27T00:30:46Z

← Older revision		Revision as of 00:30, 27 July 2010
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	The following keywords are recognised, where n and x are integer and real data, respectively.		The following keywords are recognised, where n and x are integer and real data, respectively.

			EXAMPLES FOR SPLITTING KEYWORDS UP:

			=== A-F ===
			=== G-L ===
			=== M-R ===
			=== S-Z ===

			OR

			=== AMBER keywords (old implementation) ===
			=== AMBER9 keywords ===
			=== CHARMM keywords ===
			=== AMH keywords ===

	* [[2D]]: enforce two-dimensional `flatland'.		* [[2D]]: enforce two-dimensional `flatland'.