Replication data for "Rocking (and shuttling) in a nanosized metallobox"

DOI

In this repository you will find data regarding the system parametrization, the input for molecular dynamics simulations performed with Amber, and the input files for metadynamics simulations with Plumed and Gromacs.

METHODOLOGICAL INFORMATION

  1. Description of the methods used to collect and generate the data: Guassian 16 was used for structure optimization of both host and guests N,N'-di(6-hexenyl)-naphthalenetetracarboxy-diimide (refered as NC6 or guest2), and naphthalenediimide (also refered to as NDI, NTCDI or guest4). AmberTools22 was used to generate the Amber parameters and topology files. Molecular dynamics calculations were performed with Amber24 Metadynamics calculations were performed with GROMACS and Plumed2.0

  2. Software or instruments needed to interpret the data: The data contained in this repository is all in open format. Any molecular visualization software will be able to read pdb, prmtop, inpcrd, top *gro files.

Identifier
DOI https://doi.org/10.34810/data2435
Related Identifier IsSupplementTo https://doi.org/10.1002/anie.202514744
Metadata Access https://dataverse.csuc.cat/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.34810/data2435
Provenance
Creator Ibáñez, Susana ORCID logo; Alemany Chavarria, Mercè ORCID logo; Dawe, Louise (ORCID: 0000-0003-3630-990X); Ujaque, Gregori ORCID logo; Peris, Eduardo ORCID logo
Publisher CORA.Repositori de Dades de Recerca
Contributor Alemany Chavarria, Mercè; Universitat Autònoma Barcelona
Publication Year 2026
Funding Reference https://ror.org/003x0zc53 PID2021-127862NB-I00 ; https://ror.org/003x0zc53 PID2023-150881NB-I00 ; https://ror.org/003x0zc53 PRE2021-098376
Rights CC BY-NC-SA 4.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/licenses/by-nc-sa/4.0
OpenAccess true
Contact Alemany Chavarria, Mercè (Universitat Autònoma de Barcelona)
Representation
Resource Type Simulation data; Dataset
Format text/plain; application/octet-stream; chemical/x-mol2; application/mac-compactpro; text/plain; charset=US-ASCII; text/x-fixed-field; text/x-python; application/x-msdos-program; text/x-log; application/x-shellscript; application/x-aportisdoc; chemical/x-pdb
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Version 1.0
Discipline Chemistry; Natural Sciences