GAFit - Revision history

Jorge at 23:11, 6 December 2022

2022-12-06T23:11:08Z

Jorge: /* GAFit has been used in the works */

2022-12-06T23:00:29Z

‎GAFit has been used in the works

Jorge: /* GAFit has been used in the works */

2022-12-06T22:58:12Z

‎GAFit has been used in the works

Jorge: /* GAFit has been used in the works */

2022-12-06T22:57:09Z

‎GAFit has been used in the works

Jorge: /* GAFit has been used in the works */

2022-12-06T22:56:10Z

‎GAFit has been used in the works

Jorge: /* GAFit has been used in the works */

2022-12-06T22:55:33Z

‎GAFit has been used in the works

Jorge: /* GAFit has been used in the works */

2022-12-06T22:54:33Z

‎GAFit has been used in the works

Jorge at 22:51, 6 December 2022

2022-12-06T22:51:35Z

Wikiadmin: Created page with "TOC ==GAFit== We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was a..."

2022-11-07T19:53:53Z

Created page with "__TOC__ ==GAFit== We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was a..."

New page

__TOC__
==GAFit==
We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was also interfaced with the CHARMM and MOPAC programs in order to facilitate force field parameterizations and fittings of specific reaction parameters (SRP) for semiempirical Hamiltonians.

It may be applied to a wide range of fitting problems, though it has been especially designed to significantly reduce the hard work involved in the development of potential energy surfaces for complex systems. For this purpose, it has been equipped with several programs to help the user in the preparation of the input files.

We showcase the application of the computational tool to several chemical-relevant problems: force-field parameterization, with emphasis on nonbonded energy terms or intermolecular potentials, derivation of SRP for semiempirical Hamiltonians, and fittings of generic analytical functions[https://www.sciencedirect.com/science/article/pii/S0010465517300607].

The last version, 1.6b, introduces a new module named ''generic''. This module's target is to interface a broad range of external programs with a litte effort from the user.

==Downloads==
Download the [[Media:GAFitSimplifiedUserGuide.pdf| Simplified User Guide ]]<br />
The most recent version of the User Manual (1.6) can be [[Media:Usermanual.pdf | donwloaded here ]]<br />
The most recent version of GAFit (1.6c) can be [[Media:Gafit-1.6c.tar.gz| downloaded here ]]<br />

== Authors==
Roberto Rodriguez-Fernandez, Francisco Baptista Pereira, [https://apps.uc.pt/mypage/faculty/qtmarque/en Jorge M. C. Marques ], Saulo Vázquez-Rodríguez, Emilio Martínez-Núñez

Return to [[Main_Page]]

@@ Line 26: / Line 26: @@
 * '''A Trajectory-Based Method to Explore Reaction Mechanisms''', Saulo A Vázquez, Xose Luis Otero, Emilio Martinez-Nuñez, Molecules 23(12):3156, 2018. DOI: 10.3390/molecules23123156
-* '''Exploring the first‐shell and second‐shell structures arising in the microsolvation of Li+ by rare gases''', Wanderson Silva Jesus, J. M. C. Marques, Frederico V. Prudente, Francisco B. Pereira, International Journal of Quantum Chemistry 119(20):e25860, 2018. DOI: 10.1002/qua.25860
+* '''Exploring the first‐shell and second‐shell structures arising in the microsolvation of Li<sup>+</sup> by rare gases''', Wanderson Silva Jesus, J. M. C. Marques, Frederico V. Prudente, Francisco B. Pereira, International Journal of Quantum Chemistry 119(20):e25860, 2018. DOI: 10.1002/qua.25860
 * '''GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces''', R. Rodríguez-Fernández, F.B. Pereira, J.M.C. Marques, E. Martínez-Núñez, S.A. Vázquez, Computer Physics Communications 417, 89-98, 2017. DOI: 10.1016/j.cpc.2017.02.008
-* '''Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with ﬂuorinated self-assembled monolayers''', Juan José Nogueira, Antonio Sánchez-Coronilla, Jorge M. C. Marques, William L. Hase, Emilio Martínez-Núñez, Saulo A. Vázquez, Chemical Physics 399, 193-204, 2012. DOI: 10.1016/j.chemphys.2011.02.014
+* '''Intermolecular potentials for simulations of collisions of SiNCS<sup>+</sup> and (CH<sub>3</sub>)<sub>2</sub>SiNCS<sup>+</sup> ions with ﬂuorinated self-assembled monolayers''', Juan José Nogueira, Antonio Sánchez-Coronilla, Jorge M. C. Marques, William L. Hase, Emilio Martínez-Núñez, Saulo A. Vázquez, Chemical Physics 399, 193-204, 2012. DOI: 10.1016/j.chemphys.2011.02.014
 * '''Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. The ground state of RbCs''', M.M. Almeida, F.V. Prudente, C.E. Fellows, J.M.C. Marques, F.B. Pereira, Journal of Physics B: Atomic, Molecular and Optical Physics 44, 225102, 2011. DOI: 10.1088/0953-4075/44/22/225102

@@ Line 20: / Line 20: @@
 GAFit, either in its present or earlier versions, has been used in the following papers:
-* '''The PM6-FGC Method: Improved Corrections for Amines and Amides''', Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
+* '''The PM6-FGC Method: Improved Corrections for Amines and Amides''', Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez, Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
-* '''New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling''', Sergio Pérez-Tabero, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez, Saulo A. Vázquez Journal of Chemical Theory and Computation 17(9), 5556–5567, 2021. DOI: 10.1021/acs.jctc.1c00365
+* '''New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling''', Sergio Pérez-Tabero, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez, Saulo A. Vázquez, Journal of Chemical Theory and Computation 17(9), 5556–5567, 2021. DOI: 10.1021/acs.jctc.1c00365
-* A Trajectory-Based Method to Explore Reaction Mechanisms
+* '''A Trajectory-Based Method to Explore Reaction Mechanisms''', Saulo A Vázquez, Xose Luis Otero, Emilio Martinez-Nuñez, Molecules 23(12):3156, 2018. DOI: 10.3390/molecules23123156
-* Exploring the first‐shell and second‐shell structures arising in the microsolvation of Li+ by rare gases
+* '''Exploring the first‐shell and second‐shell structures arising in the microsolvation of Li+ by rare gases''', Wanderson Silva Jesus, J. M. C. Marques, Frederico V. Prudente, Francisco B. Pereira, International Journal of Quantum Chemistry 119(20):e25860, 2018. DOI: 10.1002/qua.25860
-* GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces
+* '''GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces''', R. Rodríguez-Fernández, F.B. Pereira, J.M.C. Marques, E. Martínez-Núñez, S.A. Vázquez, Computer Physics Communications 417, 89-98, 2017. DOI: 10.1016/j.cpc.2017.02.008
-* Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with ﬂuorinated self-assembled monolayers
+* '''Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with ﬂuorinated self-assembled monolayers''', Juan José Nogueira, Antonio Sánchez-Coronilla, Jorge M. C. Marques, William L. Hase, Emilio Martínez-Núñez, Saulo A. Vázquez, Chemical Physics 399, 193-204, 2012. DOI: 10.1016/j.chemphys.2011.02.014
-* Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. The ground state of RbCs
+* '''Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. The ground state of RbCs''', M.M. Almeida, F.V. Prudente, C.E. Fellows, J.M.C. Marques, F.B. Pereira, Journal of Physics B: Atomic, Molecular and Optical Physics 44, 225102, 2011. DOI: 10.1088/0953-4075/44/22/225102
-* A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data
+* '''A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data''', J.M.C. Marques, F.V. Prudente, F.B. Pereira, M.M. Almeida, A.M. Maniero, C.E. Fellows, Journal of Physics B: Atomic, Molecular and Optical Physics 41 (8), 085103, 2008. DOI: 10.1088/0953-4075/41/8/085103
 <br />
 Return to [[Main_Page]]

@@ Line 20: / Line 20: @@
 GAFit, either in its present or earlier versions, has been used in the following papers:
-* The PM6-FGC Method: Improved Corrections for Amines and Amides Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
+* '''The PM6-FGC Method: Improved Corrections for Amines and Amides''', Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
-* New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling
+* '''New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling''', Sergio Pérez-Tabero, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez, Saulo A. Vázquez Journal of Chemical Theory and Computation 17(9), 5556–5567, 2021. DOI: 10.1021/acs.jctc.1c00365
 * A Trajectory-Based Method to Explore Reaction Mechanisms

@@ Line 20: / Line 20: @@
 GAFit, either in its present or earlier versions, has been used in the following papers:
-* The PM6-FGC Method: Improved Corrections for Amines and Amides
+* The PM6-FGC Method: Improved Corrections for Amines and Amides Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
 * New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling

@@ Line 21: / Line 21: @@
 * The PM6-FGC Method: Improved Corrections for Amines and Amides
-  Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez
+ Martiño Ríos-García, Berta Fernández, Jesús Rodríguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. Vázquez
-  Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
+ Molecules 27(5):1678, 2022. DOI: 10.3390/molecules27051678
 * New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling
-  Sergio Pérez-Tabero, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez, Saulo A. Vázquez
+Sergio Pérez-Tabero, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez, Saulo A. Vázquez
-  Journal of Chemical Theory and Computation 17(9), 5556–5567, 2021. DOI: 10.1021/acs.jctc.1c00365
+Journal of Chemical Theory and Computation 17(9), 5556–5567, 2021. DOI: 10.1021/acs.jctc.1c00365
 * A Trajectory-Based Method to Explore Reaction Mechanisms
-  Saulo A Vázquez, Xose Luis Otero, Emilio Martinez-Nuñez
+Saulo A Vázquez, Xose Luis Otero, Emilio Martinez-Nuñez
-  Molecules 23(12):3156, 2018. DOI: 10.3390/molecules23123156
+Molecules 23(12):3156, 2018. DOI: 10.3390/molecules23123156
 * Exploring the first‐shell and second‐shell structures arising in the microsolvation of Li+ by rare gases

@@ Line 16: / Line 16: @@
 == Authors==
 Roberto Rodriguez-Fernandez, Francisco Baptista Pereira, [https://apps.uc.pt/mypage/faculty/qtmarque/en  Jorge M. C. Marques ], Saulo Vázquez-Rodríguez, Emilio Martínez-Núñez
 Return to [[Main_Page]]

GAFit - Revision history

Jorge at 23:11, 6 December 2022

Jorge: /* GAFit has been used in the works */

Jorge: /* GAFit has been used in the works */

Jorge: /* GAFit has been used in the works */

Jorge: /* GAFit has been used in the works */

Jorge: /* GAFit has been used in the works */

Jorge: /* GAFit has been used in the works */

Jorge at 22:51, 6 December 2022

Wikiadmin: Created page with "__TOC__ ==GAFit== We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was a..."

Wikiadmin: Created page with "TOC ==GAFit== We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was a..."