{"id":673,"date":"2022-04-25T02:23:01","date_gmt":"2022-04-25T02:23:01","guid":{"rendered":"https:\/\/architect.oceanwp.org\/?page_id=673"},"modified":"2025-12-18T13:13:52","modified_gmt":"2025-12-18T13:13:52","slug":"portfolio","status":"publish","type":"page","link":"https:\/\/software.qui.uc.pt\/?page_id=673","title":{"rendered":"GAFit"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"673\" class=\"elementor elementor-673\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-c7bde32 elementor-section-height-min-height elementor-section-boxed elementor-section-height-default elementor-section-items-middle\" data-id=\"c7bde32\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-8ca406c\" data-id=\"8ca406c\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-fb64808 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"fb64808\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5c316fb elementor-widget elementor-widget-heading\" data-id=\"5c316fb\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">GAFit<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t<div class=\"elementor-element elementor-element-ccdb8b7 e-flex e-con-boxed e-con e-parent\" data-id=\"ccdb8b7\" data-element_type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-61c8390 elementor-widget elementor-widget-heading\" data-id=\"61c8390\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">GAFit<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e80c2fb elementor-widget__width-inherit elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"e80c2fb\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-955cc48 elementor-widget elementor-widget-text-editor\" data-id=\"955cc48\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>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.<\/p><p>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.<\/p><p>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<a class=\"external autonumber\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0010465517300607\" rel=\"nofollow\">[1]<\/a>.<\/p><p>The last version, 1.6b, introduces a new module named <i>generic<\/i>. This module&#8217;s target is to interface a broad range of external programs with a litte effort from the user.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9edd0e9 elementor-widget elementor-widget-heading\" data-id=\"9edd0e9\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">Download<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8d94383 elementor-widget__width-inherit elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"8d94383\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c0aed05 elementor-widget elementor-widget-text-editor\" data-id=\"c0aed05\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h2><strong>GAFit (1.6c)<\/strong><\/h2><p>Download the <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2023\/12\/GAFitSimplifiedUserGuide.pdf\">GAFitSimplifiedUserGuide<\/a><br \/>The most recent version of the User Manual (1.6) can be <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2023\/12\/Usermanual.pdf\">Usermanual<\/a><br \/>The most recent version of GAFit (1.6c) can be <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2023\/12\/Gafit-1.6c.tar.gz\"> downloaded here<\/a><\/p><h2><strong>GAFit (2024a)<\/strong><\/h2><p>Download the <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2024\/03\/GAFitSimplifiedUserGuide_2024a.pdf\">GAFitSimplifiedUserGuide<\/a><br \/>The most recent version of the User Manual (2024a) can be <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2024\/03\/usermanual_2024a.pdf\">Usermanual<\/a><br \/>The most recent version of GAFit (2024a) can be <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2024\/03\/gafit-2024a.tar.gz\"> downloaded here<\/a><\/p><h2>GAFit (2025m)<\/h2><p>The most recent version of GAFit (2025m) can be <a href=\"https:\/\/software.qui.uc.pt\/wp-content\/uploads\/2025\/12\/gafit-2025m.tar.gz\"> downloaded here<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e9d7fde elementor-widget elementor-widget-heading\" data-id=\"e9d7fde\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">GAFit has been used in the works<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4536f75 elementor-widget__width-inherit elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"4536f75\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-19c22ed elementor-widget elementor-widget-text-editor\" data-id=\"19c22ed\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>GAFit, either in its present or earlier versions, has been used in the following papers:<\/p><ul><li><b>The PM6-FGC Method: Improved Corrections for Amines and Amides<\/b>, Marti\u00f1o R\u00edos-Garc\u00eda, Berta Fern\u00e1ndez, Jes\u00fas Rodr\u00edguez-Otero, Enrique M. Cabaleiro-Lago, Saulo A. V\u00e1zquez, Molecules 27(5):1678, 2022. DOI: 10.3390\/molecules27051678<\/li><\/ul><ul><li><b>New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling<\/b>, Sergio P\u00e9rez-Tabero, Berta Fern\u00e1ndez, Enrique M. Cabaleiro-Lago, Emilio Mart\u00ednez-N\u00fa\u00f1ez, Saulo A. V\u00e1zquez, Journal of Chemical Theory and Computation 17(9), 5556\u20135567, 2021. DOI: 10.1021\/acs.jctc.1c00365<\/li><\/ul><ul><li><b>A Trajectory-Based Method to Explore Reaction Mechanisms<\/b>, Saulo A V\u00e1zquez, Xose Luis Otero, Emilio Martinez-Nu\u00f1ez, Molecules 23(12):3156, 2018. DOI: 10.3390\/molecules23123156<\/li><\/ul><ul><li><b>Exploring the first\u2010shell and second\u2010shell structures arising in the microsolvation of Li<sup>+<\/sup> by rare gases<\/b>, 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<\/li><\/ul><ul><li><b>GAFit: a general-purpose, user-friendly program for fitting potential energy surfaces<\/b>, R. Rodr\u00edguez-Fern\u00e1ndez, F.B. Pereira, J.M.C. Marques, E. Mart\u00ednez-N\u00fa\u00f1ez, S.A. V\u00e1zquez, Computer Physics Communications 417, 89-98, 2017. DOI: 10.1016\/j.cpc.2017.02.008<\/li><\/ul><ul><li><b>Intermolecular potentials for simulations of collisions of SiNCS<sup>+<\/sup> and (CH<sub>3<\/sub>)<sub>2<\/sub>SiNCS<sup>+<\/sup> ions with \ufb02uorinated self-assembled monolayers<\/b>, Juan Jos\u00e9 Nogueira, Antonio S\u00e1nchez-Coronilla, Jorge M. C. Marques, William L. Hase, Emilio Mart\u00ednez-N\u00fa\u00f1ez, Saulo A. V\u00e1zquez, Chemical Physics 399, 193-204, 2012. DOI: 10.1016\/j.chemphys.2011.02.014<\/li><li><b>Direct fit of spectroscopic data of diatomic molecules by using genetic algorithms: II. The ground state of RbCs<\/b>, 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<\/li><li><b>A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data<\/b>, 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<\/li><\/ul>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-4260f8c elementor-section-height-min-height elementor-section-boxed elementor-section-height-default elementor-section-items-middle\" data-id=\"4260f8c\" data-element_type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-dd3d6cb\" data-id=\"dd3d6cb\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-363901a elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"363901a\" data-element_type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3c0f214 elementor-widget elementor-widget-heading\" data-id=\"3c0f214\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">Authors<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-234219f elementor-widget elementor-widget-text-editor\" data-id=\"234219f\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>Roberto Rodriguez-Fernandez, Francisco Baptista Pereira, <a class=\"external text\" href=\"https:\/\/apps.uc.pt\/mypage\/faculty\/qtmarque\/en\" rel=\"nofollow\">Jorge M. C. Marques <\/a>, Saulo V\u00e1zquez-Rodr\u00edguez, Emilio Mart\u00ednez-N\u00fa\u00f1ez<\/p><p>Return to <a title=\"Main Page\" href=\"https:\/\/software.qui.uc.pt\/\">Main_Page<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>GAFit 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. [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ocean_post_layout":"full-screen","ocean_both_sidebars_style":"","ocean_both_sidebars_content_width":0,"ocean_both_sidebars_sidebars_width":0,"ocean_sidebar":"0","ocean_second_sidebar":"0","ocean_disable_margins":"on","ocean_add_body_class":"","ocean_shortcode_before_top_bar":"","ocean_shortcode_after_top_bar":"","ocean_shortcode_before_header":"","ocean_shortcode_after_header":"","ocean_has_shortcode":"","ocean_shortcode_after_title":"","ocean_shortcode_before_footer_widgets":"","ocean_shortcode_after_footer_widgets":"","ocean_shortcode_before_footer_bottom":"","ocean_shortcode_after_footer_bottom":"","ocean_display_top_bar":"off","ocean_display_header":"default","ocean_header_style":"transparent","ocean_center_header_left_menu":"0","ocean_custom_header_template":"0","ocean_custom_logo":0,"ocean_custom_retina_logo":0,"ocean_custom_logo_max_width":0,"ocean_custom_logo_tablet_max_width":0,"ocean_custom_logo_mobile_max_width":0,"ocean_custom_logo_max_height":0,"ocean_custom_logo_tablet_max_height":0,"ocean_custom_logo_mobile_max_height":0,"ocean_header_custom_menu":"0","ocean_menu_typo_font_family":"0","ocean_menu_typo_font_subset":"","ocean_menu_typo_font_size":0,"ocean_menu_typo_font_size_tablet":0,"ocean_menu_typo_font_size_mobile":0,"ocean_menu_typo_font_size_unit":"px","ocean_menu_typo_font_weight":"","ocean_menu_typo_font_weight_tablet":"","ocean_menu_typo_font_weight_mobile":"","ocean_menu_typo_transform":"","ocean_menu_typo_transform_tablet":"","ocean_menu_typo_transform_mobile":"","ocean_menu_typo_line_height":0,"ocean_menu_typo_line_height_tablet":0,"ocean_menu_typo_line_height_mobile":0,"ocean_menu_typo_line_height_unit":"","ocean_menu_typo_spacing":0,"ocean_menu_typo_spacing_tablet":0,"ocean_menu_typo_spacing_mobile":0,"ocean_menu_typo_spacing_unit":"","ocean_menu_link_color":"#ffffff","ocean_menu_link_color_hover":"#6e8fef","ocean_menu_link_color_active":"#ffffff","ocean_menu_link_background":"","ocean_menu_link_hover_background":"","ocean_menu_link_active_background":"","ocean_menu_social_links_bg":"","ocean_menu_social_hover_links_bg":"","ocean_menu_social_links_color":"#ffffff","ocean_menu_social_hover_links_color":"#6e8fef","ocean_disable_title":"on","ocean_disable_heading":"default","ocean_post_title":"","ocean_post_subheading":"","ocean_post_title_style":"","ocean_post_title_background_color":"","ocean_post_title_background":0,"ocean_post_title_bg_image_position":"","ocean_post_title_bg_image_attachment":"","ocean_post_title_bg_image_repeat":"","ocean_post_title_bg_image_size":"","ocean_post_title_height":0,"ocean_post_title_bg_overlay":0.5,"ocean_post_title_bg_overlay_color":"","ocean_disable_breadcrumbs":"off","ocean_breadcrumbs_color":"","ocean_breadcrumbs_separator_color":"","ocean_breadcrumbs_links_color":"","ocean_breadcrumbs_links_hover_color":"","ocean_display_footer_widgets":"off","ocean_display_footer_bottom":"off","ocean_custom_footer_template":"0","footnotes":""},"class_list":["post-673","page","type-page","status-publish","hentry","entry"],"_links":{"self":[{"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/pages\/673","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=673"}],"version-history":[{"count":61,"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/pages\/673\/revisions"}],"predecessor-version":[{"id":1143,"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=\/wp\/v2\/pages\/673\/revisions\/1143"}],"wp:attachment":[{"href":"https:\/\/software.qui.uc.pt\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=673"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}