Martignac: computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
December 2, 2024
|
| In: |
Journal of chemical information and modeling
Year: 2024, Volume: 64, Issue: 24, Pages: 9413-9423 |
| ISSN: | 1549-960X |
| DOI: | 10.1021/acs.jcim.4c01754 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1021/acs.jcim.4c01754 Verlag, lizenzpflichtig, Volltext: https://pubs.acs.org/doi/10.1021/acs.jcim.4c01754 
|
| Author Notes: | Tristan Bereau, Luis J. Walter, and Joseph F. Rudzinski |
MARC
| LEADER | 00000naa a2200000 c 4500 | ||
|---|---|---|---|
| 001 | 1927973201 | ||
| 003 | DE-627 | ||
| 005 | 20250611143348.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 250611s2024 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1021/acs.jcim.4c01754 |2 doi | |
| 035 | |a (DE-627)1927973201 | ||
| 035 | |a (DE-599)KXP1927973201 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rda | ||
| 041 | |a eng | ||
| 084 | |a 29 |2 sdnb | ||
| 100 | 1 | |a Bereau, Tristan |e VerfasserIn |0 (DE-588)1322458626 |0 (DE-627)1882396340 |4 aut | |
| 245 | 1 | 0 | |a Martignac |b computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations |c Tristan Bereau, Luis J. Walter, and Joseph F. Rudzinski |
| 264 | 1 | |c December 2, 2024 | |
| 300 | |b Illustrationen | ||
| 300 | |a 11 | ||
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a Computermedien |b c |2 rdamedia | ||
| 338 | |a Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Gesehen am 11.06.2025 | ||
| 520 | |a Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation─from system preparation to property calculations. Martignac connects to NOMAD, such that all simulation data generated are automatically normalized and stored according to the FAIR principles. We present several prototypical Martini workflows, including system generation of simple liquids and bilayers, as well as free-energy calculations for solute solvation in homogeneous liquids and drug permeation in lipid bilayers. By connecting to the NOMAD database to automatically pull existing simulations and push any new simulation generated, Martignac contributes to improving the sustainability and reproducibility of molecular simulations. | ||
| 700 | 1 | |a Walter, Luis J. |e VerfasserIn |0 (DE-588)1368412106 |0 (DE-627)1927973929 |4 aut | |
| 700 | 1 | |a Rudzinski, Joseph |e VerfasserIn |0 (DE-588)132245826X |0 (DE-627)1882395468 |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of chemical information and modeling |d Washington, DC : American Chemical Society, 2005 |g 64(2024), 24, Seite 9413-9423 |h Online-Ressource |w (DE-627)302467327 |w (DE-600)1491237-5 |w (DE-576)090855124 |x 1549-960X |7 nnas |a Martignac computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations |
| 773 | 1 | 8 | |g volume:64 |g year:2024 |g number:24 |g pages:9413-9423 |g extent:11 |a Martignac computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations |
| 856 | 4 | 0 | |u https://doi.org/10.1021/acs.jcim.4c01754 |x Verlag |x Resolving-System |z lizenzpflichtig |3 Volltext |
| 856 | 4 | 0 | |u https://pubs.acs.org/doi/10.1021/acs.jcim.4c01754 |x Verlag |z lizenzpflichtig |3 Volltext |
| 951 | |a AR | ||
| 992 | |a 20250611 | ||
| 993 | |a Article | ||
| 994 | |a 2024 | ||
| 998 | |g 1368412106 |a Walter, Luis J. |m 1368412106:Walter, Luis J. |d 130000 |d 130300 |d 130000 |e 130000PW1368412106 |e 130300PW1368412106 |e 130000PW1368412106 |k 0/130000/ |k 1/130000/130300/ |k 0/130000/ |p 2 | ||
| 998 | |g 1322458626 |a Bereau, Tristan |m 1322458626:Bereau, Tristan |d 130000 |d 130300 |e 130000PB1322458626 |e 130300PB1322458626 |k 0/130000/ |k 1/130000/130300/ |p 1 |x j | ||
| 999 | |a KXP-PPN1927973201 |e 473319093X | ||
| BIB | |a Y | ||
| SER | |a journal | ||
| JSO | |a {"relHost":[{"title":[{"title":"Journal of chemical information and modeling","title_sort":"Journal of chemical information and modeling"}],"note":["Gesehen am 03.05.2023"],"disp":"Martignac computational workflows for reproducible, traceable, and composable coarse-grained Martini simulationsJournal of chemical information and modeling","type":{"bibl":"periodical","media":"Online-Ressource"},"recId":"302467327","language":["eng"],"pubHistory":["Volume 45, issue 1 (January 2005)-"],"part":{"extent":"11","text":"64(2024), 24, Seite 9413-9423","volume":"64","issue":"24","pages":"9413-9423","year":"2024"},"origin":[{"publisherPlace":"Washington, DC","publisher":"American Chemical Society","dateIssuedDisp":"[2005]-"}],"id":{"eki":["302467327"],"zdb":["1491237-5"],"issn":["1549-960X"]},"physDesc":[{"extent":"Online-Ressource"}]}],"physDesc":[{"noteIll":"Illustrationen","extent":"11 S."}],"id":{"eki":["1927973201"],"doi":["10.1021/acs.jcim.4c01754"]},"origin":[{"dateIssuedKey":"2024","dateIssuedDisp":"December 2, 2024"}],"name":{"displayForm":["Tristan Bereau, Luis J. Walter, and Joseph F. Rudzinski"]},"language":["eng"],"recId":"1927973201","note":["Gesehen am 11.06.2025"],"type":{"media":"Online-Ressource","bibl":"article-journal"},"title":[{"subtitle":"computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations","title":"Martignac","title_sort":"Martignac"}],"person":[{"family":"Bereau","given":"Tristan","display":"Bereau, Tristan","roleDisplay":"VerfasserIn","role":"aut"},{"display":"Walter, Luis J.","roleDisplay":"VerfasserIn","role":"aut","family":"Walter","given":"Luis J."},{"role":"aut","roleDisplay":"VerfasserIn","display":"Rudzinski, Joseph","given":"Joseph","family":"Rudzinski"}]} | ||
| SRT | |a BEREAUTRISMARTIGNAC2202 | ||