{"id":"https://openalex.org/W4288052230","doi":"https://doi.org/10.1021/acs.jpcb.2c03765","title":"Gaussian Accelerated Molecular Dynamics in OpenMM","display_name":"Gaussian Accelerated Molecular Dynamics in OpenMM","publication_year":2022,"publication_date":"2022-07-27","ids":{"openalex":"https://openalex.org/W4288052230","doi":"https://doi.org/10.1021/acs.jpcb.2c03765","pmid":"https://pubmed.ncbi.nlm.nih.gov/35895977","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9773147"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jpcb.2c03765","doi":"https://doi.org/10.1021/acs.jpcb.2c03765","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jpcb.2c03765","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Physical Chemistry B","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9773147","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064345408","display_name":"Matthew M. Copeland","orcid":"https://orcid.org/0000-0002-0696-4746","observed_orcids":["https://orcid.org/0000-0002-0696-4746"]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew M. Copeland","raw_affiliation_strings":["Center for Computational Biology, University of Kansas, Lawrence, Kansas 66047, United States"],"raw_orcid":"https://orcid.org/0000-0002-0696-4746","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, University of Kansas, Lawrence, Kansas 66047, United States","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032388901","display_name":"Hung Nguyen Do","orcid":"https://orcid.org/0000-0002-6497-4096","observed_orcids":["https://orcid.org/0000-0002-6497-4096"]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hung N. Do","raw_affiliation_strings":["Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037136118","display_name":"Lane William Votapka","orcid":"https://orcid.org/0000-0002-0865-5867","observed_orcids":["https://orcid.org/0000-0002-0865-5867"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lane Votapka","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States"],"raw_orcid":"https://orcid.org/0000-0002-0865-5867","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Keya Joshi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keya Joshi","raw_affiliation_strings":["Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102817270","display_name":"Jinan Wang","orcid":"https://orcid.org/0000-0003-0162-212X","observed_orcids":["https://orcid.org/0000-0003-0162-212X"]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinan Wang","raw_affiliation_strings":["Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States"],"raw_orcid":"https://orcid.org/0000-0003-0162-212X","affiliations":[{"raw_affiliation_string":"Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081468273","display_name":"Rommie E. Amaro","orcid":"https://orcid.org/0000-0002-9275-9553","observed_orcids":["https://orcid.org/0000-0002-9275-9553"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rommie E. Amaro","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States"],"raw_orcid":"https://orcid.org/0000-0002-9275-9553","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055831887","display_name":"Yinglong Miao","orcid":"https://orcid.org/0000-0003-3714-1395","observed_orcids":["https://orcid.org/0000-0003-3714-1395","https://orcid.org/0000-0002-9809-5428"]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yinglong Miao","raw_affiliation_strings":["Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States"],"raw_orcid":"https://orcid.org/0000-0003-3714-1395","affiliations":[{"raw_affiliation_string":"Center for Computational Biology \u00a0and\u00a0 Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055831887"],"corresponding_institution_ids":["https://openalex.org/I146416000"],"apc_list":null,"apc_paid":null,"fwci":1.3852,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.80498935,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"126","issue":"31","first_page":"5810","last_page":"5820"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9326000213623047,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9326000213623047,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.029100000858306885,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.026000000536441803,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gaussian-accelerated-molecular-dynamics","display_name":"Gaussian accelerated molecular dynamics","score":0.9950000047683716},{"id":"https://openalex.org/keywords/openmm","display_name":"OpenMM","score":0.8370000123977661},{"id":"https://openalex.org/keywords/enhanced-sampling","display_name":"enhanced sampling","score":0.7860000133514404},{"id":"https://openalex.org/keywords/free-energy-calculations","display_name":"free energy calculation","score":0.8270000219345093},{"id":"https://openalex.org/keywords/alanine-dipeptide","display_name":"alanine dipeptide","score":0.9599999785423279},{"id":"https://openalex.org/keywords/rna-folding","display_name":"RNA folding","score":0.9819999933242798},{"id":"https://openalex.org/keywords/rna-tetraloop","display_name":"RNA tetraloop","score":0.8659999966621399},{"id":"https://openalex.org/keywords/hiv-1-tar-rna","display_name":"HIV-1 TAR RNA","score":0.8550000190734863},{"id":"https://openalex.org/keywords/hydrogen-bonding","display_name":"hydrogen bonding","score":0.8199999928474426},{"id":"https://openalex.org/keywords/base-stacking","display_name":"base stacking","score":0.9729999899864197},{"id":"https://openalex.org/keywords/electrostatic-interactions","display_name":"electrostatic interactions","score":0.8330000042915344}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7897657155990601},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.6495208740234375},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5917199850082397},{"id":"https://openalex.org/C2780004032","wikidata":"https://www.wikidata.org/wiki/Q6485978","display_name":"Langevin dynamics","level":2,"score":0.5615630149841309},{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.512677788734436},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4815821647644043},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.4622919261455536},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4269059896469116},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3739888072013855},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3501073122024536},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3029816746711731},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.28429630398750305},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2594399154186249},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23448112607002258},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.22257289290428162},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11773520708084106},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000409","descriptor_name":"Alanine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jpcb.2c03765","doi":"https://doi.org/10.1021/acs.jpcb.2c03765","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jpcb.2c03765","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Physical Chemistry B","raw_type":"journal-article"},{"id":"pmid:35895977","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35895977","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The journal of physical chemistry. B","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9773147","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9773147","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"J Phys Chem B","raw_type":"Text"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt4pn638w4","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/4pn638w4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"The Journal of Physical Chemistry B, vol 126, iss 31","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9773147","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9773147","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"J Phys Chem B","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1205355600","display_name":null,"funder_award_id":"R01GM132572","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G3226045097","display_name":null,"funder_award_id":"ACI-1 548 562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4991932250","display_name":"A MULTISCALE APPROACH TO TARGET THE ACHILLES HEEL OF P53 CANCER MUTANTS","funder_award_id":"R01GM132826","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G505115660","display_name":"Enhanced Sampling of G-Protein-Coupled Receptor-G Protein Interactions","funder_award_id":"R01GM132572","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6047471812","display_name":null,"funder_award_id":"DE-AC02-05-CH11231","funder_id":"https://openalex.org/F4320310514","funder_display_name":"Department of Energy and Climate Change"},{"id":"https://openalex.org/G7224823057","display_name":null,"funder_award_id":"R01GM132826","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G8379721793","display_name":"A public workflow for predicting peptide binding structures","funder_award_id":"2121063","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320310131","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57"},{"id":"https://openalex.org/F4320310514","display_name":"Department of Energy and Climate Change","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W136462871","https://openalex.org/W1178456644","https://openalex.org/W1530166615","https://openalex.org/W1964412608","https://openalex.org/W1976203248","https://openalex.org/W1976499671","https://openalex.org/W1976548894","https://openalex.org/W1985775264","https://openalex.org/W1989429077","https://openalex.org/W1992105696","https://openalex.org/W1992899488","https://openalex.org/W1993177346","https://openalex.org/W1999522888","https://openalex.org/W2004822259","https://openalex.org/W2016856091","https://openalex.org/W2018643516","https://openalex.org/W2020851807","https://openalex.org/W2021520922","https://openalex.org/W2029667189","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2038354555","https://openalex.org/W2039369142","https://openalex.org/W2039781258","https://openalex.org/W2040809566","https://openalex.org/W2041616872","https://openalex.org/W2042821667","https://openalex.org/W2048792281","https://openalex.org/W2048822589","https://openalex.org/W2052126522","https://openalex.org/W2063636398","https://openalex.org/W2066531623","https://openalex.org/W2066951434","https://openalex.org/W2075460992","https://openalex.org/W2078055239","https://openalex.org/W2078253946","https://openalex.org/W2081046982","https://openalex.org/W2082586732","https://openalex.org/W2093221728","https://openalex.org/W2100627460","https://openalex.org/W2103325328","https://openalex.org/W2106140689","https://openalex.org/W2112154906","https://openalex.org/W2121111513","https://openalex.org/W2206954826","https://openalex.org/W2313116527","https://openalex.org/W2332712348","https://openalex.org/W2335200606","https://openalex.org/W2463238596","https://openalex.org/W2530696470","https://openalex.org/W2560839684","https://openalex.org/W2744122781","https://openalex.org/W2788789259","https://openalex.org/W2794209945","https://openalex.org/W2892113269","https://openalex.org/W2921808963","https://openalex.org/W2957275001","https://openalex.org/W2973252091","https://openalex.org/W2979875716","https://openalex.org/W2996960886","https://openalex.org/W3033732543","https://openalex.org/W3042908073","https://openalex.org/W3044187902","https://openalex.org/W3086801715","https://openalex.org/W3094004932","https://openalex.org/W3130785256","https://openalex.org/W3135534391","https://openalex.org/W3157703588","https://openalex.org/W3160431173","https://openalex.org/W3186331361","https://openalex.org/W4210763131","https://openalex.org/W4214643185","https://openalex.org/W4220983722","https://openalex.org/W4223488106"],"related_works":["https://openalex.org/W2744122781","https://openalex.org/W1178456644","https://openalex.org/W2560839684","https://openalex.org/W3135534391","https://openalex.org/W7202122373","https://openalex.org/W4318069730","https://openalex.org/W4412087221","https://openalex.org/W2803489728","https://openalex.org/W2739546689","https://openalex.org/W7155751305"],"abstract_inverted_index":{"Gaussian":[0],"accelerated":[1],"molecular":[2,61],"dynamics":[3,62],"(GaMD)":[4],"is":[5],"a":[6],"computational":[7],"technique":[8],"that":[9],"provides":[10],"both":[11,93],"unconstrained":[12],"enhanced":[13],"sampling":[14],"and":[15,33,42,80,82,104,124],"free":[16,54],"energy":[17,55],"calculations":[18],"of":[19,26,39,57,73,84,94,121],"biomolecules.":[20,126],"Here,":[21],"we":[22],"present":[23],"the":[24,29,70,85,89],"implementation":[25],"GaMD":[27,50,67,111],"in":[28,112,119],"OpenMM":[30,113],"simulation":[31],"package":[32],"validate":[34],"it":[35],"on":[36],"model":[37],"systems":[38],"alanine":[40,46],"dipeptide":[41],"RNA":[43,76],"folding.":[44],"For":[45],"dipeptide,":[47],"30":[48],"ns":[49,59],"production":[51],"simulations":[52,68,120],"reproduced":[53],"profiles":[56],"1000":[58],"conventional":[60],"(cMD)":[63],"simulations.":[64],"In":[65],"addition,":[66],"captured":[69],"folding":[71],"pathways":[72],"three":[74],"hyperstable":[75],"tetraloops":[77],"(UUCG,":[78],"GCAA,":[79],"CUUG)":[81],"binding":[83],"rbt203":[86],"ligand":[87],"to":[88],"HIV-1":[90],"Tar":[91],"RNA,":[92,123],"which":[95],"involved":[96],"critical":[97],"electrostatic":[98],"interactions":[99],"such":[100],"as":[101],"hydrogen":[102],"bonding":[103],"base":[105],"stacking.":[106],"Together":[107],"with":[108],"previous":[109],"implementations,":[110],"will":[114],"allow":[115],"for":[116],"wider":[117],"applications":[118],"proteins,":[122],"other":[125]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":8}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2022-07-28T00:00:00"}