ChargeCalculator:Terminology - Revision history

Crina: /* Charge set */

2015-05-29T16:39:44Z

Charge set

← Older revision		Revision as of 16:39, 29 May 2015
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	== Charge set ==		== Charge set ==
	Each job produces a ~~distinct~~ '''set of charges'''~~, with~~ a unique ID encoding the EEM parameter set, method and total molecular charge. If the original input file contained values of atomic charges, these are also stored in a charge set named according to the input file, and marked by the tag ''ref''. All charge sets are available for analysis in ACC.		Each job produces a '''set of charges''' identified by a unique ID encoding the EEM parameter set, method and total molecular charge. If the original input file contained values of atomic charges, these are also stored in a charge set named according to the input file, and marked by the tag ''ref''. All charge sets are available for analysis in ACC.


	'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* EEM parameter sets */

2015-05-29T16:37:39Z

EEM parameter sets

← Older revision		Revision as of 16:37, 29 May 2015
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	== EEM parameter sets ==		== EEM parameter sets ==
	A '''set of EEM parameters''', or '''EEM parameter set''', represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development. The ~~fitting procedure mainly affects the~~ accuracy of ~~the~~ EEM parameter set~~, meaning~~ the ability of the EEM ~~parameter set~~ to reproduce the reference QM data.		A '''set of EEM parameters''', or '''EEM parameter set''', represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development. The accuracy of an EEM parameter set is thus evaluated as the ability of the resulting EEM charges to reproduce the reference QM data.

	== Computation method ==		== Computation method ==

Crina: /* Charges */

2015-05-29T16:33:36Z

Charges

← Older revision		Revision as of 16:33, 29 May 2015
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	= Charges =		= Charges =

	ACC operates with charges at several ~~resolutions~~.		ACC operates with charges at several levels of resolution.

	== Atomic charge ==		== Atomic charge ==

Crina: /* Molecular charge */

2014-12-30T20:53:48Z

Molecular charge

← Older revision		Revision as of 20:53, 30 December 2014
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	== Molecular charge ==		== Molecular charge ==
	The '''total molecular charge''' is a formal value based on the molecular structure and the protonation state of all ionizable groups. The process of atomic charge calculation in ACC consists of distributing the amount of electron density given by the '''total molecular charge''' across the molecule, to each atom based on certain criteria and algorithms. Thus, the sum of atomic charges ~~for~~ over atoms in a molecule equals the molecular charge. Similarly, the sum of residue charges over all residues in a molecule equals the molecular charge.		The '''total molecular charge''' is a formal value based on the molecular structure and the protonation state of all ionizable groups. The process of atomic charge calculation in ACC consists of distributing the amount of electron density given by the '''total molecular charge''' across the molecule, to each atom based on certain criteria and algorithms. Thus, the sum of atomic charges over all atoms in a molecule equals the total molecular charge. Similarly, the sum of residue charges over all residues in a molecule equals the total molecular charge.

	= Work flow =		= Work flow =

Crina: /* Work flow */

2014-12-08T12:15:35Z

Work flow

← Older revision		Revision as of 12:15, 8 December 2014
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	= Work flow =		= Work flow =
	The work flow of atomic charge calculation in ACC ~~requires~~ is based on a few key terms.		The work flow of atomic charge calculation in ACC is based on a few key terms.

	== Atom type ==		== Atom type ==
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	==Atom type scheme==		==Atom type scheme==
	An '''atom type scheme''' attempts to group atoms according to ''atom type'' by using some unified set of descriptors. ACC is currently able to distinguish two types of '''atom type schemes''', namely according to ''chemical elements'', and according to ''chemical elements and bond order''.		An '''atom type scheme''' attempts to group atoms according to ''atom type'' by using some unified set of descriptors. ACC is currently able to distinguish two types of '''atom type schemes''', namely according to ''chemical elements'' (C,H,O...), and according to ''chemical elements and bond order'' (C1, C2, H1, O1, O2...).

	== EEM parameters ==		== EEM parameters ==

Crina: /* Job */

2014-11-29T05:36:18Z

Job

← Older revision		Revision as of 05:36, 29 November 2014
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	== Job ==		== Job ==
	A '''job''' is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. A single ACC ''computation'' may consist of multiple '''jobs''', and all ''output files'' are thus named according to the job ID.		An atomic charge calculation '''job''' in ACC is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. A single ACC ''computation'' may consist of multiple '''jobs''', and all ''output files'' are thus named according to the job ID.

	== Charge set ==		== Charge set ==

Crina: /* Job */

2014-11-29T05:35:52Z

Job

← Older revision		Revision as of 05:35, 29 November 2014
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	== Job ==		== Job ==
	A '''job''' is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. ~~All~~ ''output files'' are named according to the job ID.		A '''job''' is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. A single ACC ''computation'' may consist of multiple '''jobs''', and all ''output files'' are thus named according to the job ID.

	== Charge set ==		== Charge set ==

Crina: /* Work flow */

2014-11-29T05:34:18Z

Work flow

← Older revision		Revision as of 05:34, 29 November 2014
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	== Computation method ==		== Computation method ==
			The '''computation method''' refers to the EEM implementation that will be used during the atomic charge calculation (see also the [[ChargeCalculator:Theoretical_background \| theoretical background]]), along with related computation ''options'' specific to each method. ACC implements the classical EEM formalism, along with two EEM approximations which increase time and memory efficiency, and allow real time calculations for extremely large biomacromolecular complexes.

	~~== Computation parameters ==~~


	== Job ==		== Job ==
			A '''job''' is defined based on the molecule and its total charge, along with the EEM parameter set and computation method used. All ''output files'' are named according to the job ID.

	== Charge set ==		== Charge set ==
			Each job produces a distinct '''set of charges''', with a unique ID encoding the EEM parameter set, method and total molecular charge. If the original input file contained values of atomic charges, these are also stored in a charge set named according to the input file, and marked by the tag ''ref''. All charge sets are available for analysis in ACC.


	'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''		'''Return to the [[ChargeCalculator:UserManual \| Table of contents]].'''

Crina: /* EEM parameter sets */

2014-11-29T05:21:37Z

EEM parameter sets

← Older revision		Revision as of 05:21, 29 November 2014
Line 37:		Line 37:

	== EEM parameter sets ==		== EEM parameter sets ==
	A '''set of EEM parameters''', or '''EEM parameter set''' represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development. The fitting procedure mainly affects the accuracy of the EEM parameter set, meaning the ability of the EEM parameter set to reproduce the reference QM data.		A '''set of EEM parameters''', or '''EEM parameter set''', represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development. The fitting procedure mainly affects the accuracy of the EEM parameter set, meaning the ability of the EEM parameter set to reproduce the reference QM data.

	== Computation method ==		== Computation method ==

Crina: /* EEM parameter sets */

2014-11-29T05:20:42Z

EEM parameter sets

← Older revision		Revision as of 05:20, 29 November 2014
Line 37:		Line 37:

	== EEM parameter sets ==		== EEM parameter sets ==
	A '''set of EEM parameters''', or '''EEM parameter set''' represents a collection of EEM parameters		A '''set of EEM parameters''', or '''EEM parameter set''' represents a collection of EEM parameters that has been developed for a certain group of target molecules, using a certain kind of reference data and a certain kind of fitting procedure. An EEM parameter set generally covers atom types for H,C,N,O, but also halogens, metals, etc, depending on the molecules targetted during the development of the EEM parameters. Reference data generally comes from high level Quantum Mechanical (QM) calculations. The applicability domain of an EEM parameter set is closely related to the applicability domain of the reference QM data used during the development. The fitting procedure mainly affects the accuracy of the EEM parameter set, meaning the ability of the EEM parameter set to reproduce the reference QM data.

	An EEM parameter set generally covers H,C,N,O, but also halogens, metals, etc, depending on ~~what type of~~ molecules ~~were~~ targetted during the development of the EEM parameters.

	== Computation method ==		== Computation method ==