{"id":73279,"date":"2019-01-31T22:42:36","date_gmt":"2019-01-31T22:42:36","guid":{"rendered":"https:\/\/sossogroup.uk\/?post_type=portfolio&p=73279"},"modified":"2019-07-31T20:15:04","modified_gmt":"2019-07-31T20:15:04","slug":"heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2","status":"publish","type":"portfolio","link":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/","title":{"rendered":"Promoting transparency and reproducibility in enhanced molecular simulations"},"content":{"rendered":"
[vc_row][vc_column width=”1\/1″][vc_column_text]\r\n

Nature Methods<\/strong><\/span><\/h3>\r\n

Just accepted<\/i><\/p>\r\n

DOI: 10.1038\/s41592-019-0506-8<\/a><\/p>\r\n\r\n\r\n\r\n

Alright, hold your horses. My contribution to this ginormous (the words you learn from your kids…) effort is tiny – but it’s there! In a nutshell, the amazing people at the very core of the continuous, painstaking, never-ending development and expansion of the PLUMED software, have righteously decided to “outline [their] efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations”. Via PLUMED, obviously. What’s that I hear (very few of you) ask – well, PLUMED is “an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations”. Check it out here<\/a>. Now, all this is good – in fact, exceptionally good. First of all, because the unsung heroes at the heart of this PLUMED\u00a0endeavour are excellent<\/em> scientists.\u00a0Massimiliano Bonomi<\/a>,\u00a0Giovanni Bussi<\/a>,\u00a0Carlo Camilloni<\/a>,\u00a0Gareth Tribello<\/a> – it doesn’t get much better than the stuff these guys do, and I mean it. As an example, it is because of Gareth that much of my ice-related research has come to life. You can have some decent ideas, but then you also need some code capable to deal with some rather cumbersome science – PLUMED can do that for you. It interfaces with basically everything under the sun, and can compute almost everything you can think about – if not, ask the community: it really works! Ok, enough with the violins. Have a look at the paper online<\/a>, or grab a .pdf<\/a>. Most importantly, get a sense of what can be done with PLUMED by navigating through the plethora of working examples (most of them related to published works) contained in the PLUMED-NEST<\/a>. Happy enhanced sampling!<\/p>\r\n[\/vc_column_text][\/vc_column][\/vc_row]<\/div>","protected":false},"excerpt":{"rendered":"

Nature Methods<\/strong><\/span><\/h3>\n

Just accepted<\/i><\/p>\n

DOI: 10.1038\/s41592-019-0506-8<\/a><\/p>\n

<\/p>\n

<\/p>\n

Alright, hold your horses. My contribution to this ginormous (the words you learn from your kids…) effort is tiny – but it’s there! In a nutshell, the amazing people at the very core of the continuous, painstaking, never-ending development and expansion of the PLUMED software, have righteously decided to “outline [their] efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations”. Via PLUMED, obviously. What’s that I hear (very few of you) ask – well, PLUMED is “an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations”. Check it out here<\/a>. Now, all this is good – in fact, exceptionally good. First of all, because the unsung heroes at the heart of this PLUMED\u00a0endeavour are excellent<\/em> scientists.\u00a0Massimiliano Bonomi<\/a>,\u00a0Giovanni Bussi<\/a>,\u00a0Carlo Camilloni<\/a>,\u00a0Gareth Tribello<\/a> – it doesn’t get much better than the stuff these guys do, and I mean it. As an example, it is because of Gareth that much of my ice-related research has come to life. You can have some decent ideas, but then you also need some code capable to deal with some rather cumbersome science – PLUMED can do that for you. It interfaces with basically everything under the sun, and can compute almost everything you can think about – if not, ask the community: it really works! Ok, enough with the violins. Have a look at the paper online<\/a>, or grab a .pdf<\/a>. Most importantly, get a sense of what can be done with PLUMED by navigating through the plethora of working examples (most of them related to published works) contained in the PLUMED-NEST<\/a>. Happy enhanced sampling!<\/p>\n","protected":false},"author":2,"featured_media":73316,"parent":0,"menu_order":0,"template":"","meta":{"_acf_changed":false},"portfolio_category":[],"acf":[],"yoast_head":"\nPromoting transparency and reproducibility in enhanced molecular simulations - Sosso Group<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Promoting transparency and reproducibility in enhanced molecular simulations - Sosso Group\" \/>\n<meta property=\"og:description\" content=\"Nature Methods Just accepted DOI: 10.1038\/s41592-019-0506-8 Alright, hold your horses. My contribution to this ginormous (the words you learn from your kids...) effort is tiny - but it's there! In a nutshell, the amazing people at the very core of the continuous, painstaking, never-ending development and expansion of the PLUMED software, have righteously decided to "outline [their] efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations". Via PLUMED, obviously. What's that I hear (very few of you) ask - well, PLUMED is "an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations". Check it out here. Now, all this is good - in fact, exceptionally good. First of all, because the unsung heroes at the heart of this PLUMED\u00a0endeavour are excellent scientists.\u00a0Massimiliano Bonomi,\u00a0Giovanni Bussi,\u00a0Carlo Camilloni,\u00a0Gareth Tribello - it doesn't get much better than the stuff these guys do, and I mean it. As an example, it is because of Gareth that much of my ice-related research has come to life. You can have some decent ideas, but then you also need some code capable to deal with some rather cumbersome science - PLUMED can do that for you. It interfaces with basically everything under the sun, and can compute almost everything you can think about - if not, ask the community: it really works! Ok, enough with the violins. Have a look at the paper online, or grab a .pdf. Most importantly, get a sense of what can be done with PLUMED by navigating through the plethora of working examples (most of them related to published works) contained in the PLUMED-NEST. Happy enhanced sampling!\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/\" \/>\n<meta property=\"og:site_name\" content=\"Sosso Group\" \/>\n<meta property=\"article:modified_time\" content=\"2019-07-31T20:15:04+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png\" \/>\n\t<meta property=\"og:image:width\" content=\"562\" \/>\n\t<meta property=\"og:image:height\" content=\"290\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@sossogroup\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/\",\"url\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/\",\"name\":\"Promoting transparency and reproducibility in enhanced molecular simulations - Sosso Group\",\"isPartOf\":{\"@id\":\"https:\/\/sossogroup.uk\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png\",\"datePublished\":\"2019-01-31T22:42:36+00:00\",\"dateModified\":\"2019-07-31T20:15:04+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage\",\"url\":\"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png\",\"contentUrl\":\"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png\",\"width\":562,\"height\":290},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/sossogroup.uk\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Portfolio\",\"item\":\"https:\/\/sossogroup.uk\/portfolio\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Promoting transparency and reproducibility in enhanced molecular simulations\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/sossogroup.uk\/#website\",\"url\":\"https:\/\/sossogroup.uk\/\",\"name\":\"Sosso Group\",\"description\":\"Molecular Simulations of Disordered Systems and Phase Transitions\",\"publisher\":{\"@id\":\"https:\/\/sossogroup.uk\/#\/schema\/person\/e586dca382ee4c8f83d900f37413cfff\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/sossogroup.uk\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":[\"Person\",\"Organization\"],\"@id\":\"https:\/\/sossogroup.uk\/#\/schema\/person\/e586dca382ee4c8f83d900f37413cfff\",\"name\":\"Dr Gabriele C. 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And, in reverse order of importance: Avid Cyclist Massive Tolkien fan Husband & Father of Two\",\"sameAs\":[\"https:\/\/sossogroup.uk\",\"https:\/\/twitter.com\/https:\/\/twitter.com\/sossogroup\"]}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Promoting transparency and reproducibility in enhanced molecular simulations - Sosso Group","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/","og_locale":"en_US","og_type":"article","og_title":"Promoting transparency and reproducibility in enhanced molecular simulations - Sosso Group","og_description":"Nature Methods Just accepted DOI: 10.1038\/s41592-019-0506-8 Alright, hold your horses. My contribution to this ginormous (the words you learn from your kids...) effort is tiny - but it's there! In a nutshell, the amazing people at the very core of the continuous, painstaking, never-ending development and expansion of the PLUMED software, have righteously decided to \"outline [their] efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations\". Via PLUMED, obviously. What's that I hear (very few of you) ask - well, PLUMED is \"an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations\". Check it out here. Now, all this is good - in fact, exceptionally good. First of all, because the unsung heroes at the heart of this PLUMED\u00a0endeavour are excellent scientists.\u00a0Massimiliano Bonomi,\u00a0Giovanni Bussi,\u00a0Carlo Camilloni,\u00a0Gareth Tribello - it doesn't get much better than the stuff these guys do, and I mean it. 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Happy enhanced sampling!","og_url":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/","og_site_name":"Sosso Group","article_modified_time":"2019-07-31T20:15:04+00:00","og_image":[{"width":562,"height":290,"url":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png","type":"image\/png"}],"twitter_card":"summary_large_image","twitter_site":"@sossogroup","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/","url":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/","name":"Promoting transparency and reproducibility in enhanced molecular simulations - Sosso Group","isPartOf":{"@id":"https:\/\/sossogroup.uk\/#website"},"primaryImageOfPage":{"@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage"},"image":{"@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage"},"thumbnailUrl":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png","datePublished":"2019-01-31T22:42:36+00:00","dateModified":"2019-07-31T20:15:04+00:00","breadcrumb":{"@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#primaryimage","url":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png","contentUrl":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/Screen-Shot-2019-07-31-at-22.02.13.png","width":562,"height":290},{"@type":"BreadcrumbList","@id":"https:\/\/sossogroup.uk\/portfolio\/heterogeneous-seeded-molecular-dynamics-as-a-tool-to-probe-the-ice-nucleating-ability-of-crystalline-surfaces-4-2-2\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/sossogroup.uk\/"},{"@type":"ListItem","position":2,"name":"Portfolio","item":"https:\/\/sossogroup.uk\/portfolio\/"},{"@type":"ListItem","position":3,"name":"Promoting transparency and reproducibility in enhanced molecular simulations"}]},{"@type":"WebSite","@id":"https:\/\/sossogroup.uk\/#website","url":"https:\/\/sossogroup.uk\/","name":"Sosso Group","description":"Molecular Simulations of Disordered Systems and Phase Transitions","publisher":{"@id":"https:\/\/sossogroup.uk\/#\/schema\/person\/e586dca382ee4c8f83d900f37413cfff"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/sossogroup.uk\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"},{"@type":["Person","Organization"],"@id":"https:\/\/sossogroup.uk\/#\/schema\/person\/e586dca382ee4c8f83d900f37413cfff","name":"Dr Gabriele C. Sosso","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/sossogroup.uk\/#\/schema\/person\/image\/","url":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/prof_1.jpeg","contentUrl":"https:\/\/sossogroup.uk\/wp-content\/uploads\/2018\/01\/prof_1.jpeg","width":2048,"height":1367,"caption":"Dr Gabriele C. Sosso"},"logo":{"@id":"https:\/\/sossogroup.uk\/#\/schema\/person\/image\/"},"description":"Assistant Professor in Computational Chemistry I am a computational scientist, chiefly interested in the physical chemistry of condensed matter, from supercooled liquids to biological interfaces. My vision is to understand the chemistry, the functional properties and the phase transitions of different classes of systems, from metallic glasses to cellular membranes. My approach consists in performing fundamental research using computer simulations, aimed at rationalise, complement and guide experiments and applications. 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