Skip to content

Commit

Permalink
Merge pull request #4844 from openjournals/joss.05989
Browse files Browse the repository at this point in the history
Merging automatically
  • Loading branch information
editorialbot authored Dec 15, 2023
2 parents 11a2e92 + bd19a55 commit 5e020f0
Show file tree
Hide file tree
Showing 3 changed files with 1,038 additions and 0 deletions.
364 changes: 364 additions & 0 deletions joss.05989/10.21105.joss.05989.crossref.xml
Original file line number Diff line number Diff line change
@@ -0,0 +1,364 @@
<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1"
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
xmlns:rel="http://www.crossref.org/relations.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
version="5.3.1"
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd">
<head>
<doi_batch_id>20231215T175157-3c8de5de5a5464db188e168f7403fec2ee0b6a08</doi_batch_id>
<timestamp>20231215175156</timestamp>
<depositor>
<depositor_name>JOSS Admin</depositor_name>
<email_address>[email protected]</email_address>
</depositor>
<registrant>The Open Journal</registrant>
</head>
<body>
<journal>
<journal_metadata>
<full_title>Journal of Open Source Software</full_title>
<abbrev_title>JOSS</abbrev_title>
<issn media_type="electronic">2475-9066</issn>
<doi_data>
<doi>10.21105/joss</doi>
<resource>https://joss.theoj.org</resource>
</doi_data>
</journal_metadata>
<journal_issue>
<publication_date media_type="online">
<month>12</month>
<year>2023</year>
</publication_date>
<journal_volume>
<volume>8</volume>
</journal_volume>
<issue>92</issue>
</journal_issue>
<journal_article publication_type="full_text">
<titles>
<title>FlowerMD: Flexible Library of Organic Workflows and
Extensible Recipes for Molecular Dynamics</title>
</titles>
<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Marjan</given_name>
<surname>Albooyeh</surname>
<ORCID>https://orcid.org/0009-0001-9565-3076</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Chris</given_name>
<surname>Jones</surname>
<ORCID>https://orcid.org/0000-0002-6196-5274</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Rainier</given_name>
<surname>Barrett</surname>
<ORCID>https://orcid.org/0000-0002-5728-9074</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Eric</given_name>
<surname>Jankowski</surname>
<ORCID>https://orcid.org/0000-0002-3267-1410</ORCID>
</person_name>
</contributors>
<publication_date>
<month>12</month>
<day>15</day>
<year>2023</year>
</publication_date>
<pages>
<first_page>5989</first_page>
</pages>
<publisher_item>
<identifier id_type="doi">10.21105/joss.05989</identifier>
</publisher_item>
<ai:program name="AccessIndicators">
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
</ai:program>
<rel:program>
<rel:related_item>
<rel:description>Software archive</rel:description>
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.10215501</rel:inter_work_relation>
</rel:related_item>
<rel:related_item>
<rel:description>GitHub review issue</rel:description>
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/5989</rel:inter_work_relation>
</rel:related_item>
</rel:program>
<doi_data>
<doi>10.21105/joss.05989</doi>
<resource>https://joss.theoj.org/papers/10.21105/joss.05989</resource>
<collection property="text-mining">
<item>
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.05989.pdf</resource>
</item>
</collection>
</doi_data>
<citation_list>
<citation key="radonpy_2022">
<article_title>RadonPy: Automated physical property
calculation using all-atom classical molecular dynamics simulations for
polymer informatics</article_title>
<author>Hayashi</author>
<journal_title>npj Computational Materials</journal_title>
<issue>1</issue>
<volume>8</volume>
<doi>10.1038/s41524-022-00906-4</doi>
<issn>2057-3960</issn>
<cYear>2022</cYear>
<unstructured_citation>Hayashi, Y., Shiomi, J., Morikawa,
J., &amp; Yoshida, R. (2022). RadonPy: Automated physical property
calculation using all-atom classical molecular dynamics simulations for
polymer informatics. Npj Computational Materials, 8(1), 222.
https://doi.org/10.1038/s41524-022-00906-4</unstructured_citation>
</citation>
<citation key="TRUE_2020">
<article_title>Towards molecular simulations that are
transparent, reproducible, usable by others, and extensible
(TRUE)</article_title>
<author>Thompson</author>
<journal_title>Molecular Physics</journal_title>
<issue>9</issue>
<volume>118</volume>
<doi>10.1080/00268976.2020.1742938</doi>
<issn>0026-8976</issn>
<cYear>2020</cYear>
<unstructured_citation>Thompson, M. W., Gilmer, J. B.,
Matsumoto, R. A., Quach, C. D., Shamaprasad, P., Yang, A. H., Iacovella,
C. R., McCabe, C., &amp; Cummings, P. T. (2020). Towards molecular
simulations that are transparent, reproducible, usable by others, and
extensible (TRUE). Molecular Physics, 118(9), e1742938.
https://doi.org/10.1080/00268976.2020.1742938</unstructured_citation>
</citation>
<citation key="biosimspace_2019">
<article_title>BioSimSpace: An interoperable python
framework for biomolecular simulation</article_title>
<author>Hedges</author>
<journal_title>Journal of Open Source
Software</journal_title>
<issue>43</issue>
<volume>4</volume>
<doi>10.21105/joss.01831</doi>
<issn>2475-9066</issn>
<cYear>2019</cYear>
<unstructured_citation>Hedges, L., Mey, A., Laughton, C.,
Gervasio, F., Mulholland, A., Woods, C., &amp; Michel, J. (2019).
BioSimSpace: An interoperable python framework for biomolecular
simulation. Journal of Open Source Software, 4(43), 1831.
https://doi.org/10.21105/joss.01831</unstructured_citation>
</citation>
<citation key="anderson2020hoomd">
<article_title>HOOMD-blue: A python package for
high-performance molecular dynamics and hard particle monte carlo
simulations</article_title>
<author>Anderson</author>
<journal_title>Computational Materials
Science</journal_title>
<volume>173</volume>
<doi>10.1016/j.commatsci.2019.109363</doi>
<cYear>2020</cYear>
<unstructured_citation>Anderson, J. A., Glaser, J., &amp;
Glotzer, S. C. (2020). HOOMD-blue: A python package for high-performance
molecular dynamics and hard particle monte carlo simulations.
Computational Materials Science, 173, 109363.
https://doi.org/10.1016/j.commatsci.2019.109363</unstructured_citation>
</citation>
<citation key="polyply_2022">
<article_title>Polyply; a python suite for facilitating
simulations of macromolecules and nanomaterials</article_title>
<author>Grünewald</author>
<journal_title>Nature Communications</journal_title>
<issue>1</issue>
<volume>13</volume>
<doi>10.1038/s41467-021-27627-4</doi>
<issn>2041-1723</issn>
<cYear>2022</cYear>
<unstructured_citation>Grünewald, F., Alessandri, R., Kroon,
P. C., Monticelli, L., Souza, P. C. T., &amp; Marrink, S. J. (2022).
Polyply; a python suite for facilitating simulations of macromolecules
and nanomaterials. Nature Communications, 13(1), 68.
https://doi.org/10.1038/s41467-021-27627-4</unstructured_citation>
</citation>
<citation key="eastman2017openmm">
<article_title>OpenMM 7: Rapid development of high
performance algorithms for molecular dynamics</article_title>
<author>Eastman</author>
<journal_title>PLoS computational biology</journal_title>
<issue>7</issue>
<volume>13</volume>
<doi>10.1371/journal.pcbi.1005659</doi>
<cYear>2017</cYear>
<unstructured_citation>Eastman, P., Swails, J., Chodera, J.
D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett,
A. C., Harrigan, M. P., Stern, C. D., &amp; others. (2017). OpenMM 7:
Rapid development of high performance algorithms for molecular dynamics.
PLoS Computational Biology, 13(7), e1005659.
https://doi.org/10.1371/journal.pcbi.1005659</unstructured_citation>
</citation>
<citation key="Santana-Bonilla_2023">
<article_title>Modular software for generating and modeling
diverse polymer databases</article_title>
<author>Santana-Bonilla</author>
<journal_title>Journal of Chemical Information and
Modeling</journal_title>
<issue>12</issue>
<volume>63</volume>
<doi>10.1021/acs.jcim.3c00081</doi>
<issn>1549-9596</issn>
<cYear>2023</cYear>
<unstructured_citation>Santana-Bonilla, A., López-Ríos De
Castro, R., Sun, P., Ziolek, R. M., &amp; Lorenz, C. D. (2023). Modular
software for generating and modeling diverse polymer databases. Journal
of Chemical Information and Modeling, 63(12), 3761–3771.
https://doi.org/10.1021/acs.jcim.3c00081</unstructured_citation>
</citation>
<citation key="martin2018pyprism">
<article_title>pyPRISM: A computational tool for
liquid-state theory calculations of macromolecular
materials</article_title>
<author>Martin</author>
<journal_title>Macromolecules</journal_title>
<issue>8</issue>
<volume>51</volume>
<doi>10.1021/acs.macromol.8b00011</doi>
<cYear>2018</cYear>
<unstructured_citation>Martin, T. B., Gartner III, T. E.,
Jones, R. L., Snyder, C. R., &amp; Jayaraman, A. (2018). pyPRISM: A
computational tool for liquid-state theory calculations of
macromolecular materials. Macromolecules, 51(8), 2906–2922.
https://doi.org/10.1021/acs.macromol.8b00011</unstructured_citation>
</citation>
<citation key="Klein2016mBuild">
<article_title>A hierarchical, component based approach to
screening properties of soft matter</article_title>
<author>Klein</author>
<journal_title>Foundations of molecular modeling and
simulation: Select papers from FOMMS 2015</journal_title>
<doi>10.1007/978-981-10-1128-3_5</doi>
<isbn>978-981-10-1128-3</isbn>
<cYear>2016</cYear>
<unstructured_citation>Klein, C., Sallai, J., Jones, T. J.,
Iacovella, C. R., McCabe, C., &amp; Cummings, P. T. (2016). A
hierarchical, component based approach to screening properties of soft
matter. In R. Q. Snurr, C. S. Adjiman, &amp; D. A. Kofke (Eds.),
Foundations of molecular modeling and simulation: Select papers from
FOMMS 2015 (pp. 79–92). Springer Singapore.
https://doi.org/10.1007/978-981-10-1128-3_5</unstructured_citation>
</citation>
<citation key="lammps_2022">
<article_title>LAMMPS - a flexible simulation tool for
particle-based materials modeling at the atomic, meso, and continuum
scales</article_title>
<author>Thompson</author>
<journal_title>Computer Physics
Communications</journal_title>
<volume>271</volume>
<doi>10.1016/j.cpc.2021.108171</doi>
<cYear>2022</cYear>
<unstructured_citation>Thompson, A. P., Aktulga, H. M.,
Berger, R., Bolintineanu, D. S., Brown, W. M., Crozier, P. S., In ’T
Veld, P. J., Kohlmeyer, A., Moore, S. G., Nguyen, T. D., Shan, R.,
Stevens, M. J., Tranchida, J., Trott, C., &amp; Plimpton, S. J. (2022).
LAMMPS - a flexible simulation tool for particle-based materials
modeling at the atomic, meso, and continuum scales. Computer Physics
Communications, 271, 108171.
https://doi.org/10.1016/j.cpc.2021.108171</unstructured_citation>
</citation>
<citation key="gmso">
<article_title>GMSO: General Molecular Simulation
Object</article_title>
<author>Thompson</author>
<doi>10.5281/zenodo.8370982</doi>
<cYear>2023</cYear>
<unstructured_citation>Thompson, M., Yang, A., Matsumoto,
R., Timalsina, U., Quach, C., CalCraven, Shamaprasad, P., Gilmer, J.,
DeFever, R. S., Chris, J., Dice, B., Crawford, B., Iacovella, C.,
Albooyeh, M., Smith, R., Bansal, A., Marin-Rimoldi, E., &amp; zijiewu3.
(2023). GMSO: General Molecular Simulation Object (Version 0.11.2).
https://doi.org/10.5281/zenodo.8370982</unstructured_citation>
</citation>
<citation key="parmed">
<article_title>ParmED: Cross-program parameter and topology
file editor and molecular mechanical simulator engine</article_title>
<author>Swails</author>
<cYear>2014</cYear>
<unstructured_citation>Swails, J., Hernandez, C., Mobley, D.
L., Nguyen, H., Wang, L.-P., &amp; Janowski, P. (2014). ParmED:
Cross-program parameter and topology file editor and molecular
mechanical simulator engine (Version 4.1.0). GitHub.
https://github.com/ParmEd/ParmEd</unstructured_citation>
</citation>
<citation key="aggarwal_molecular_2020">
<article_title>Molecular dynamics studies on the strength
and ductility of symmetric thermally welded joints</article_title>
<author>Aggarwal</author>
<journal_title>Modelling and Simulation in Materials Science
and Engineering</journal_title>
<doi>10.1088/1361-651X/ab6a44</doi>
<issn>0965-0393</issn>
<cYear>2020</cYear>
<unstructured_citation>Aggarwal, I., Paul, S., Sinha, N. K.,
&amp; Basu, S. (2020). Molecular dynamics studies on the strength and
ductility of symmetric thermally welded joints. Modelling and Simulation
in Materials Science and Engineering.
https://doi.org/10.1088/1361-651X/ab6a44</unstructured_citation>
</citation>
<citation key="bukowski_load-bearing_2021">
<article_title>Load-bearing entanglements in polymer
glasses</article_title>
<author>Bukowski</author>
<journal_title>Science Advances</journal_title>
<issue>38</issue>
<volume>7</volume>
<doi>10.1126/sciadv.abg9763</doi>
<issn>2375-2548</issn>
<cYear>2021</cYear>
<unstructured_citation>Bukowski, C., Zhang, T., Riggleman,
R. A., &amp; Crosby, A. J. (2021). Load-bearing entanglements in polymer
glasses. Science Advances, 7(38), eabg9763.
https://doi.org/10.1126/sciadv.abg9763</unstructured_citation>
</citation>
<citation key="fan_wetting_1995">
<article_title>Wetting of crystalline polymer surfaces: A
molecular dynamics simulation</article_title>
<author>Fan</author>
<journal_title>The Journal of Chemical
Physics</journal_title>
<issue>20</issue>
<volume>103</volume>
<doi>10.1063/1.470016</doi>
<issn>0021-9606</issn>
<cYear>1995</cYear>
<unstructured_citation>Fan, C. F., &amp; Caǧin, T. (1995).
Wetting of crystalline polymer surfaces: A molecular dynamics
simulation. The Journal of Chemical Physics, 103(20), 9053–9061.
https://doi.org/10.1063/1.470016</unstructured_citation>
</citation>
<citation key="bamane_wetting_2021">
<article_title>Wetting simulations of high-performance
polymer resins on carbon surfaces as a function of temperature using
molecular dynamics</article_title>
<author>Bamane</author>
<journal_title>Polymers</journal_title>
<issue>13</issue>
<volume>13</volume>
<doi>10.3390/polym13132162</doi>
<issn>2073-4360</issn>
<cYear>2021</cYear>
<unstructured_citation>Bamane, S. S., Gaikwad, P. S., Radue,
M. S., Gowtham, S., &amp; Odegard, G. M. (2021). Wetting simulations of
high-performance polymer resins on carbon surfaces as a function of
temperature using molecular dynamics. Polymers, 13(13), 2162.
https://doi.org/10.3390/polym13132162</unstructured_citation>
</citation>
</citation_list>
</journal_article>
</journal>
</body>
</doi_batch>
Loading

0 comments on commit 5e020f0

Please sign in to comment.