{"_buckets": {"deposit": "9741dd13-adbf-42fc-a250-fd64b26fdc51"}, "_deposit": {"created_by": 17, "id": "2002048", "owner": "17", "owners": [17], "owners_ext": {"displayname": "\u56f3\u66f8\u60c5\u5831\u4fc2", "username": "repository"}, "pid": {"revision_id": 0, "type": "depid", "value": "2002048"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:02002048", "sets": []}, "author_link": [], "control_number": "2002048", "item_1615768549627": {"attribute_name": "\u51fa\u7248\u30bf\u30a4\u30d7", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_ab4af688f83e57aa", "subitem_version_type": "AM"}]}, "item_1629683748249": {"attribute_name": "\u65e5\u4ed8", "attribute_value_mlt": [{"subitem_date_issued_datetime": "2022-11-15", "subitem_date_issued_type": "Available"}]}, "item_9_biblio_info_6": {"attribute_name": "\u66f8\u8a8c\u60c5\u5831", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2021-11-15", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "30", "bibliographicPageEnd": "2144", "bibliographicPageStart": "2136", "bibliographicVolumeNumber": "42", "bibliographic_titles": [{"bibliographic_title": "Journal of Computational Chemistry", "bibliographic_titleLang": "en"}]}]}, "item_9_description_4": {"attribute_name": "\u5185\u5bb9\u8a18\u8ff0", "attribute_value_mlt": [{"subitem_description": "The position-dependent diffusion coefficient along with free energy profile are important parameters needed to study mass transport in heterogeneous systems such as biological and polymer membranes, and molecular dynamics (MD) calculation is a popular tool to obtain them. Among many methodologies, the Marrink\u2013Berendsen (MB) method is often employed to calculate the position-dependent diffusion coefficient, in which the autocorrelation function of the force on a fixed molecule is related to the friction on the molecule. However, the diffusion coefficient is shown to be affected by the period of the removal of the center-of-mass velocity, \u03c4v0, which is necessary when performing MD calculations using the Ewald method for Coulombic interaction. We have clarified theoretically in this study how this operation affects the diffusion coefficient calculated by the MB method, and the theoretical predictions are proven by MD calculations. Therefore, we succeeded in providing guidance on how to select an appropriate \u03c4v0 value in estimating the position-dependent diffusion coefficient by the MB method. This guideline is applicable also to the Woolf\u2013Roux method.", "subitem_description_language": "en", "subitem_description_type": "Abstract"}]}, "item_9_publisher_32": {"attribute_name": "\u51fa\u7248\u8005", "attribute_value_mlt": [{"subitem_publisher": "Wiley", "subitem_publisher_language": "en"}]}, "item_9_relation_43": {"attribute_name": "\u95a2\u9023\u60c5\u5831", "attribute_value_mlt": [{"subitem_relation_type": "isVersionOf", "subitem_relation_type_id": {"subitem_relation_type_id_text": "https://doi.org/10.1002/jcc.26742", "subitem_relation_type_select": "DOI"}}]}, "item_9_rights_12": {"attribute_name": "\u6a29\u5229", "attribute_value_mlt": [{"subitem_rights": "\"This is the peer reviewed version of the following article: [Fujimoto, K., Nagai, T., Yamaguchi, T., J. Comput. Chem. 2021, 42( 30), 2136. https://doi.org/10.1002/jcc.26742], which has been published in final form at [https://doi.org/10.1002/jcc.26742]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley\u2019s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.\"", "subitem_rights_language": "en"}]}, "item_9_source_id_7": {"attribute_name": "\u53ce\u9332\u7269\u8b58\u5225\u5b50", "attribute_value_mlt": [{"subitem_source_identifier": "0192-8651", "subitem_source_identifier_type": "PISSN"}]}, "item_access_right": {"attribute_name": "\u30a2\u30af\u30bb\u30b9\u6a29", "attribute_value_mlt": [{"subitem_access_right": "embargoed access", "subitem_access_right_uri": "http://purl.org/coar/access_right/c_f1cf"}]}, "item_creator": {"attribute_name": "\u8457\u8005", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Fujimoto, Kazushi", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Nagai, Tetsuro", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Yamaguchi, Tsuyoshi", "creatorNameLang": "en"}]}]}, "item_files": {"attribute_name": "\u30d5\u30a1\u30a4\u30eb\u60c5\u5831", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2022-11-15"}], "displaytype": "detail", "download_preview_message": "Download / Preview is available from 2022/11/14.", "file_order": 0, "filename": "main_R2_ver3.pdf", "filesize": [{"value": "796 KB"}], "format": "application/pdf", "future_date_message": "Download is available from 2022/11/14.", "is_thumbnail": false, "mimetype": "application/pdf", "size": 796000.0, "url": {"objectType": "fulltext", "url": "https://nagoya.repo.nii.ac.jp/record/2002048/files/main_R2_ver3.pdf"}, "version_id": "87660ecc-9279-463a-881e-ed34e1c96002"}]}, "item_language": {"attribute_name": "\u8a00\u8a9e", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "\u8cc7\u6e90\u30bf\u30a4\u30d7", "attribute_value_mlt": [{"resourcetype": "journal article", "resourceuri": "http://purl.org/coar/resource_type/c_6501"}]}, "item_title": "Momentum removal to obtain the position\u2010dependent diffusion constant in constrained molecular dynamics simulation", "item_titles": {"attribute_name": "\u30bf\u30a4\u30c8\u30eb", "attribute_value_mlt": [{"subitem_title": "Momentum removal to obtain the position\u2010dependent diffusion constant in constrained molecular dynamics simulation", "subitem_title_language": "en"}]}, "item_type_id": "40001", "owner": "17", "path": ["320/321/322"], "permalink_uri": "http://hdl.handle.net/2237/0002002048", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2022-02-08"}, "publish_date": "2022-02-08", "publish_status": "0", "recid": "2002048", "relation": {}, "relation_version_is_last": true, "title": ["Momentum removal to obtain the position\u2010dependent diffusion constant in constrained molecular dynamics simulation"], "weko_shared_id": -1}