Fine-tuning thermostats for coarse-grained simulations
Resumen:
When performing MD simulations, several aspects must be considered, forcefield of preference and solvent model in first place, but also when designing a protocol, among another relevant choices, the one of which thermostat to use, given the relevance of temperature control, specially if we want to reproduce melting temperatures.
| 2024 | |
| Agencia Nacional de Investigación e Innovación | |
|
Molecular Dynamics Thermostats Melting Temperature Ciencias Naturales y Exactas Ciencias Químicas Físico-Química, Ciencia de los Polímeros, Electroquímica |
|
| Inglés | |
| Institut Pasteur de Montevideo | |
| IPMON en REDI | |
| https://hdl.handle.net/20.500.12381/3621 | |
| Acceso abierto | |
| Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional. (CC BY-NC-ND) |
| _version_ | 1809796485187895296 |
|---|---|
| author | Alba, Antonella |
| author2 | Ballesteros, Andrés Soñora, Martin Silva dos Santos, Lucianna Pantano, Sergio |
| author2_role | author author author author |
| author_facet | Alba, Antonella Ballesteros, Andrés Soñora, Martin Silva dos Santos, Lucianna Pantano, Sergio |
| author_role | author |
| bitstream.checksum.fl_str_mv | 710ccfef5cb01d54b75d1d847d6b6b7b 0506c21c935146896ac61495b17b875f |
| bitstream.checksumAlgorithm.fl_str_mv | MD5 MD5 |
| bitstream.url.fl_str_mv | https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3621/2/license.txt https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3621/1/poster-conesul-Alba.pdf |
| collection | IPMON en REDI |
| dc.creator.none.fl_str_mv | Alba, Antonella Ballesteros, Andrés Soñora, Martin Silva dos Santos, Lucianna Pantano, Sergio |
| dc.date.accessioned.none.fl_str_mv | 2024-09-06T16:01:54Z |
| dc.date.available.none.fl_str_mv | 2024-09-06T16:01:54Z |
| dc.date.issued.none.fl_str_mv | 2024-08-09 |
| dc.description.abstract.none.fl_txt_mv | When performing MD simulations, several aspects must be considered, forcefield of preference and solvent model in first place, but also when designing a protocol, among another relevant choices, the one of which thermostat to use, given the relevance of temperature control, specially if we want to reproduce melting temperatures. |
| dc.description.sponsorship.none.fl_txt_mv | Agencia Nacional de Investigación e Innovación |
| dc.identifier.anii.es.fl_str_mv | POS_NAC_2022_1_173849 |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12381/3621 |
| dc.language.iso.none.fl_str_mv | eng |
| dc.rights.*.fl_str_mv | Acceso abierto |
| dc.rights.license.none.fl_str_mv | Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional. (CC BY-NC-ND) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.es.fl_str_mv | CONESUL, Universidad de Buenos Aires (UBA), Agosto 2024 |
| dc.source.none.fl_str_mv | reponame:IPMON en REDI instname:Institut Pasteur de Montevideo instacron:Institut Pasteur de Montevideo |
| dc.subject.anii.none.fl_str_mv | Ciencias Naturales y Exactas Ciencias Químicas Físico-Química, Ciencia de los Polímeros, Electroquímica |
| dc.subject.es.fl_str_mv | Molecular Dynamics Thermostats Melting Temperature |
| dc.title.none.fl_str_mv | Fine-tuning thermostats for coarse-grained simulations |
| dc.type.es.fl_str_mv | Documento de conferencia |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/conferenceObject |
| dc.type.version.es.fl_str_mv | Aceptado |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/acceptedVersion |
| description | When performing MD simulations, several aspects must be considered, forcefield of preference and solvent model in first place, but also when designing a protocol, among another relevant choices, the one of which thermostat to use, given the relevance of temperature control, specially if we want to reproduce melting temperatures. |
| eu_rights_str_mv | openAccess |
| format | conferenceObject |
| id | IPMON_7c8c09126454f2ca9710f56ed887f350 |
| identifier_str_mv | POS_NAC_2022_1_173849 |
| instacron_str | Institut Pasteur de Montevideo |
| institution | Institut Pasteur de Montevideo |
| instname_str | Institut Pasteur de Montevideo |
| language | eng |
| network_acronym_str | IPMON |
| network_name_str | IPMON en REDI |
| oai_identifier_str | oai:redi.anii.org.uy:20.500.12381/3621 |
| publishDate | 2024 |
| reponame_str | IPMON en REDI |
| repository.mail.fl_str_mv | msarroca@pasteur.edu.uy |
| repository.name.fl_str_mv | IPMON en REDI - Institut Pasteur de Montevideo |
| repository_id_str | 9421_2 |
| rights_invalid_str_mv | Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional. (CC BY-NC-ND) Acceso abierto |
| spelling | Reconocimiento-NoComercial-SinObraDerivada 4.0 Internacional. (CC BY-NC-ND)Acceso abiertoinfo:eu-repo/semantics/openAccess2024-09-06T16:01:54Z2024-09-06T16:01:54Z2024-08-09https://hdl.handle.net/20.500.12381/3621POS_NAC_2022_1_173849When performing MD simulations, several aspects must be considered, forcefield of preference and solvent model in first place, but also when designing a protocol, among another relevant choices, the one of which thermostat to use, given the relevance of temperature control, specially if we want to reproduce melting temperatures.Agencia Nacional de Investigación e InnovaciónengCONESUL, Universidad de Buenos Aires (UBA), Agosto 2024reponame:IPMON en REDIinstname:Institut Pasteur de Montevideoinstacron:Institut Pasteur de MontevideoMolecular DynamicsThermostatsMelting TemperatureCiencias Naturales y ExactasCiencias QuímicasFísico-Química, Ciencia de los Polímeros, ElectroquímicaFine-tuning thermostats for coarse-grained simulationsDocumento de conferenciaAceptadoinfo:eu-repo/semantics/acceptedVersioninfo:eu-repo/semantics/conferenceObjectInstitut Pasteur de Montevideo//Ciencias Naturales y Exactas/Ciencias Químicas/Físico-Química, Ciencia de los Polímeros, ElectroquímicaAlba, AntonellaBallesteros, AndrésSoñora, MartinSilva dos Santos, LuciannaPantano, SergioLICENSElicense.txtlicense.txttext/plain; charset=utf-85124https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3621/2/license.txt710ccfef5cb01d54b75d1d847d6b6b7bMD52ORIGINALposter-conesul-Alba.pdfposter-conesul-Alba.pdfPóster CONESUL termostatos Dinámica Molecularapplication/pdf2126817https://redi.anii.org.uy/jspui/bitstream/20.500.12381/3621/1/poster-conesul-Alba.pdf0506c21c935146896ac61495b17b875fMD5120.500.12381/36212024-09-06 13:01:57.113oai:redi.anii.org.uy:20.500.12381/3621PHA+PGI+QUNVRVJETyBERSBDRVNJT04gTk8gRVhDTFVTSVZBIERFIERFUkVDSE9TPC9iPjwvcD4NCg0KPHA+QWNlcHRhbmRvIGxhIGNlc2nDs24gZGUgZGVyZWNob3MgZWwgdXN1YXJpbyBERUNMQVJBIHF1ZSBvc3RlbnRhIGxhIGNvbmRpY2nDs24gZGUgYXV0b3IgZW4gZWwgc2VudGlkbyBxdWUgb3RvcmdhIGxhIGxlZ2lzbGFjacOzbiB2aWdlbnRlIHNvYnJlIHByb3BpZWRhZCBpbnRlbGVjdHVhbCBkZSBsYSBvYnJhIG9yaWdpbmFsIHF1ZSBlc3TDoSBlbnZpYW5kbyAo4oCcbGEgb2JyYeKAnSkuIEVuIGNhc28gZGUgc2VyIGNvdGl0dWxhciwgZWwgYXV0b3IgZGVjbGFyYSBxdWUgY3VlbnRhIGNvbiBlbCAgY29uc2VudGltaWVudG8gZGUgbG9zIHJlc3RhbnRlcyB0aXR1bGFyZXMgcGFyYSBoYWNlciBsYSBwcmVzZW50ZSBjZXNpw7NuLiBFbiBjYXNvIGRlIHByZXZpYSBjZXNpw7NuIGRlIGxvcyBkZXJlY2hvcyBkZSBleHBsb3RhY2nDs24gc29icmUgbGEgb2JyYSBhIHRlcmNlcm9zLCBlbCBhdXRvciBkZWNsYXJhIHF1ZSB0aWVuZSBsYSBhdXRvcml6YWNpw7NuIGV4cHJlc2EgZGUgZGljaG9zIHRpdHVsYXJlcyBkZSBkZXJlY2hvcyBhIGxvcyBmaW5lcyBkZSBlc3RhIGNlc2nDs24sIG8gYmllbiBxdWUgaGEgY29uc2VydmFkbyBsYSBmYWN1bHRhZCBkZSBjZWRlciBlc3RvcyBkZXJlY2hvcyBlbiBsYSBmb3JtYSBwcmV2aXN0YSBlbiBsYSBwcmVzZW50ZSBjZXNpw7NuLjwvcD4NCg0KPHA+Q29uIGVsIGZpbiBkZSBkYXIgbGEgbcOheGltYSBkaWZ1c2nDs24gYSBsYSBvYnJhIGEgdHJhdsOpcyBkZWwgcmVwb3NpdG9yaW8gZGUgYWNjZXNvIGFiaWVydG8gUkVESSAoaHR0cHM6Ly9yZWRpLmFuaWkub3JnLnV5KSwgZWwgQVVUT1IgQ0VERSBhIDxiPkFnZW5jaWEgTmFjaW9uYWwgZGUgSW52ZXN0aWdhY2nDs24gZSBJbm5vdmFjacOzbjwvYj4gKDxiPkFOSUk8L2I+KSB5IGEgPGI+SW5zdGl0dXQgUGFzdGV1ciBkZSBNb250ZXZpZGVvPC9iPiAoPGI+SVBNT048L2I+KSwgZGUgZm9ybWEgZ3JhdHVpdGEgeSBOTyBFWENMVVNJVkEsIGNvbiBjYXLDoWN0ZXIgaXJyZXZvY2FibGUgZSBpbGltaXRhZG8gZW4gZWwgdGllbXBvIHkgY29uIMOhbWJpdG8gbXVuZGlhbCwgbG9zIGRlcmVjaG9zIGRlIHJlcHJvZHVjY2nDs24sIGRlIGRpc3RyaWJ1Y2nDs24sIGRlIGNvbXVuaWNhY2nDs24gcMO6YmxpY2EsIGluY2x1aWRvIGVsIGRlcmVjaG8gZGUgcHVlc3RhIGEgZGlzcG9zaWNpw7NuIGVsZWN0csOzbmljYSwgcGFyYSBxdWUgcHVlZGEgc2VyIHV0aWxpemFkYSBkZSBmb3JtYSBsaWJyZSB5IGdyYXR1aXRhIHBvciB0b2RvcyBsb3MgcXVlIGxvIGRlc2Vlbi48L3A+DQoNCjxwPkxhIGNlc2nDs24gc2UgcmVhbGl6YSBiYWpvIGxhcyBzaWd1aWVudGVzIGNvbmRpY2lvbmVzOjwvcD4NCg0KPHA+TGEgdGl0dWxhcmlkYWQgZGUgbGEgb2JyYSBzZWd1aXLDoSBjb3JyZXNwb25kaWVuZG8gYWwgQXV0b3IgeSBsYSBwcmVzZW50ZSBjZXNpw7NuIGRlIGRlcmVjaG9zIHBlcm1pdGlyw6EgYSA8Yj5BTklJPC9iPiB5IGEgPGI+SVBNT048L2I+OjwvcD4NCg0KPHVsPg0KPGxpIHZhbHVlPShhKT5UcmFuc2Zvcm1hciBsYSBvYnJhIGVuIGxhIG1lZGlkYSBlbiBxdWUgc2VhIG5lY2VzYXJpbyBwYXJhIGFkYXB0YXJsYSBhIGN1YWxxdWllciB0ZWNub2xvZ8OtYSBzdXNjZXB0aWJsZSBkZSBpbmNvcnBvcmFjacOzbiBhIEludGVybmV0OyByZWFsaXphciBsYXMgYWRhcHRhY2lvbmVzIG5lY2VzYXJpYXMgcGFyYSBoYWNlciBwb3NpYmxlIHN1IGFjY2VzbyB5IHZpc3VhbGl6YWNpw7NuIHBlcm1hbmVudGUsIGHDum4gcG9yIHBhcnRlIGRlIHBlcnNvbmFzIGNvbiBkaXNjYXBhY2lkYWQsIHJlYWxpemFyIGxhcyBtaWdyYWNpb25lcyBkZSBmb3JtYXRvcyBwYXJhIGFzZWd1cmFyIGxhIHByZXNlcnZhY2nDs24gYSBsYXJnbyBwbGF6bywgaW5jb3Jwb3JhciBsb3MgbWV0YWRhdG9zIG5lY2VzYXJpb3MgcGFyYSByZWFsaXphciBlbCByZWdpc3RybyBkZSBsYSBvYnJhLCBlIGluY29ycG9yYXIgdGFtYmnDqW4g4oCcbWFyY2FzIGRlIGFndWHigJ0gbyBjdWFscXVpZXIgb3RybyBzaXN0ZW1hIGRlIHNlZ3VyaWRhZCBvIGRlIHByb3RlY2Npw7NuIG8gZGUgaWRlbnRpZmljYWNpw7NuIGRlIHByb2NlZGVuY2lhLiBFbiBuaW5nw7puIGNhc28gZGljaGFzIG1vZGlmaWNhY2lvbmVzIGltcGxpY2Fyw6FuIGFkdWx0ZXJhY2lvbmVzIGVuIGVsIGNvbnRlbmlkbyBkZSBsYSBvYnJhLjwvbGk+IA0KPGxpIHZhbHVlPShiKT5SZXByb2R1Y2lyIGxhIG9icmEgZW4gdW4gbWVkaW8gZGlnaXRhbCBwYXJhIHN1IGluY29ycG9yYWNpw7NuIGEgc2lzdGVtYXMgZGUgYsO6c3F1ZWRhIHkgcmVjdXBlcmFjacOzbiwgaW5jbHV5ZW5kbyBlbCBkZXJlY2hvIGEgcmVwcm9kdWNpciB5IGFsbWFjZW5hcmxhIGVuIHNlcnZpZG9yZXMgdSBvdHJvcyBtZWRpb3MgZGlnaXRhbGVzIGEgbG9zIGVmZWN0b3MgZGUgc2VndXJpZGFkIHkgcHJlc2VydmFjacOzbi48L2xpPiANCjxsaSB2YWx1ZT0oYyk+UGVybWl0aXIgYSBsb3MgdXN1YXJpb3MgbGEgZGVzY2FyZ2EgZGUgY29waWFzIGVsZWN0csOzbmljYXMgZGUgbGEgb2JyYSBlbiB1biBzb3BvcnRlIGRpZ2l0YWwuPC9saT4gDQo8bGkgdmFsdWU9KGQpPlJlYWxpemFyIGxhIGNvbXVuaWNhY2nDs24gcMO6YmxpY2EgeSBwdWVzdGEgYSBkaXNwb3NpY2nDs24gZGUgbGEgb2JyYSBhY2Nlc2libGUgZGUgbW9kbyBsaWJyZSB5IGdyYXR1aXRvIGEgdHJhdsOpcyBkZSBJbnRlcm5ldC4NCjwvdWw+DQoNCjxwPkVuIHZpcnR1ZCBkZWwgY2Fyw6FjdGVyIG5vIGV4Y2x1c2l2byBkZSBsYSBjZXNpw7NuLCBlbCBBdXRvciBjb25zZXJ2YSB0b2RvcyBsb3MgZGVyZWNob3MgZGUgYXV0b3Igc29icmUgbGEgb2JyYSwgeSBwb2Ryw6EgcG9uZXJsYSBhIGRpc3Bvc2ljacOzbiBkZWwgcMO6YmxpY28gZW4gZXN0YSB5IGVuIHBvc3RlcmlvcmVzIHZlcnNpb25lcywgYSB0cmF2w6lzIGRlIGxvcyBtZWRpb3MgcXVlIGVzdGltZSBvcG9ydHVub3MuPC9wPg0KDQo8cD5FbCBBdXRvciBkZWNsYXJhIGJham8ganVyYW1lbnRvIHF1ZSBsYSBwcmVzZW50ZSBjZXNpw7NuIG5vIGluZnJpbmdlIG5pbmfDum4gZGVyZWNobyBkZSB0ZXJjZXJvcywgeWEgc2VhbiBkZSBwcm9waWVkYWQgaW5kdXN0cmlhbCwgaW50ZWxlY3R1YWwgbyBjdWFscXVpZXIgb3RybyB5IGdhcmFudGl6YSBxdWUgZWwgY29udGVuaWRvIGRlIGxhIG9icmEgbm8gYXRlbnRhIGNvbnRyYSBsb3MgZGVyZWNob3MgYWwgaG9ub3IsIGEgbGEgaW50aW1pZGFkIHkgYSBsYSBpbWFnZW4gZGUgdGVyY2Vyb3MsIG5pIGVzIGRpc2NyaW1pbmF0b3Jpby4gPGI+QU5JSTwvYj4gZSA8Yj5JUE1PTjwvYj4gZXN0YXLDoW4gZXhlbnRhcyBkZSBsYSByZXZpc2nDs24gZGVsIGNvbnRlbmlkbyBkZSBsYSBvYnJhLCBxdWUgZW4gdG9kbyBjYXNvIHBlcm1hbmVjZXLDoSBiYWpvIGxhIHJlc3BvbnNhYmlsaWRhZCBleGNsdXNpdmEgZGVsIEF1dG9yLjwvcD4NCg0KPHA+TGEgb2JyYSBzZSBwb25kcsOhIGEgZGlzcG9zaWNpw7NuIGRlIGxvcyB1c3VhcmlvcyBwYXJhIHF1ZSBoYWdhbiBkZSBlbGxhIHVuIHVzbyBqdXN0byB5IHJlc3BldHVvc28gZGUgbG9zIGRlcmVjaG9zIGRlbCBhdXRvciB5IGNvbiBmaW5lcyBkZSBlc3R1ZGlvLCBpbnZlc3RpZ2FjacOzbiwgbyBjdWFscXVpZXIgb3RybyBmaW4gbMOtY2l0by4gRWwgbWVuY2lvbmFkbyB1c28sIG3DoXMgYWxsw6EgZGUgbGEgY29waWEgcHJpdmFkYSwgcmVxdWVyaXLDoSBxdWUgc2UgY2l0ZSBsYSBmdWVudGUgeSBzZSByZWNvbm96Y2EgbGEgYXV0b3LDrWEuIEEgdGFsZXMgZmluZXMgZWwgQXV0b3IgYWNlcHRhIGVsIHVzbyBkZSBsaWNlbmNpYXMgQ3JlYXRpdmUgQ29tbW9ucyB5IEVMSUdFIHVuYSBkZSBlc3RhcyBsaWNlbmNpYXMgZXN0YW5kYXJpemFkYXMgYSBsb3MgZmluZXMgZGUgY29tdW5pY2FyIHN1IG9icmEuPC9wPg0KDQo8cD5FbCBBdXRvciwgY29tbyBnYXJhbnRlIGRlIGxhIGF1dG9yw61hIGRlIGxhIG9icmEgeSBlbiByZWxhY2nDs24gYSBsYSBtaXNtYSwgZGVjbGFyYSBxdWUgPGI+QU5JSTwvYj4gZSA8Yj5JUE1PTjwvYj4gc2UgZW5jdWVudHJhbiBsaWJyZXMgZGUgdG9kbyB0aXBvIGRlIHJlc3BvbnNhYmlsaWRhZCwgc2VhIMOpc3RhIGNpdmlsLCBhZG1pbmlzdHJhdGl2YSBvIHBlbmFsLCB5IHF1ZSDDqWwgbWlzbW8gYXN1bWUgbGEgcmVzcG9uc2FiaWxpZGFkIGZyZW50ZSBhIGN1YWxxdWllciByZWNsYW1vIG8gZGVtYW5kYSBwb3IgcGFydGUgZGUgdGVyY2Vyb3MuIDxiPkFOSUk8L2I+IGUgPGI+SVBNT048L2I+IGVzdGFyw6FuIGV4ZW50YXMgZGUgZWplcmNpdGFyIGFjY2lvbmVzIGxlZ2FsZXMgZW4gbm9tYnJlIGRlbCBBdXRvciBlbiBlbCBzdXB1ZXN0byBkZSBpbmZyYWNjaW9uZXMgYSBkZXJlY2hvcyBkZSBwcm9waWVkYWQgaW50ZWxlY3R1YWwgZGVyaXZhZG9zIGRlbCBkZXDDs3NpdG8geSBhcmNoaXZvIGRlIGxhIG9icmEuPC9wPg0KDQo8cD48Yj5BTklJPC9iPiBlIDxiPklQTU9OPC9iPiBub3RpZmljYXLDoW4gYWwgQXV0b3IgZGUgY3VhbHF1aWVyIHJlY2xhbWFjacOzbiBxdWUgcmVjaWJhIGRlIHRlcmNlcm9zIGVuIHJlbGFjacOzbiBjb24gbGEgb2JyYSB5LCBlbiBwYXJ0aWN1bGFyLCBkZSByZWNsYW1hY2lvbmVzIHJlbGF0aXZhcyBhIGxvcyBkZXJlY2hvcyBkZSBwcm9waWVkYWQgaW50ZWxlY3R1YWwgc29icmUgZWxsYS48L3A+DQoNCjxwPkVsIEF1dG9yIHBvZHLDoSBzb2xpY2l0YXIgZWwgcmV0aXJvIG8gbGEgaW52aXNpYmlsaXphY2nDs24gZGUgbGEgb2JyYSBkZSBSRURJIHPDs2xvIHBvciBjYXVzYSBqdXN0aWZpY2FkYS4gQSB0YWwgZmluIGRlYmVyw6EgbWFuaWZlc3RhciBzdSB2b2x1bnRhZCBlbiBmb3JtYSBmZWhhY2llbnRlIHkgYWNyZWRpdGFyIGRlYmlkYW1lbnRlIGxhIGNhdXNhIGp1c3RpZmljYWRhLiBBc2ltaXNtbyA8Yj5BTklJPC9iPiBlIDxiPklQTU9OPC9iPiBwb2Ryw6FuIHJldGlyYXIgbyBpbnZpc2liaWxpemFyIGxhIG9icmEgZGUgUkVESSwgcHJldmlhIG5vdGlmaWNhY2nDs24gYWwgQXV0b3IsIGVuIHN1cHVlc3RvcyBzdWZpY2llbnRlbWVudGUganVzdGlmaWNhZG9zLCBvIGVuIGNhc28gZGUgcmVjbGFtYWNpb25lcyBkZSB0ZXJjZXJvcy48L3A+Privadahttps://pasteur.uy/https://redi.anii.org.uy/oai/requestmsarroca@pasteur.edu.uyUruguayopendoar:9421_22024-09-06T16:01:57IPMON en REDI - Institut Pasteur de Montevideofalse |
| spellingShingle | Fine-tuning thermostats for coarse-grained simulations Alba, Antonella Molecular Dynamics Thermostats Melting Temperature Ciencias Naturales y Exactas Ciencias Químicas Físico-Química, Ciencia de los Polímeros, Electroquímica |
| status_str | acceptedVersion |
| title | Fine-tuning thermostats for coarse-grained simulations |
| title_full | Fine-tuning thermostats for coarse-grained simulations |
| title_fullStr | Fine-tuning thermostats for coarse-grained simulations |
| title_full_unstemmed | Fine-tuning thermostats for coarse-grained simulations |
| title_short | Fine-tuning thermostats for coarse-grained simulations |
| title_sort | Fine-tuning thermostats for coarse-grained simulations |
| topic | Molecular Dynamics Thermostats Melting Temperature Ciencias Naturales y Exactas Ciencias Químicas Físico-Química, Ciencia de los Polímeros, Electroquímica |
| url | https://hdl.handle.net/20.500.12381/3621 |
