Mg2+-bound human oxytocin receptor bound to oxytocin

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Francesco Musiani;Samira Al Sadi;Alejandro Giorgetti;Mercedes Alfonso-Prieto;Paolo Carloni;

MD-A00400

Created: 6 Feb 2026
License: GNU Lesser General Public License (LGPL), version 2.1 (opens in a new tab)

Description

Atomistic molecular dynamics simulations on the Mg2+-bound human oxytocin receptor bound to oxytocin in explicit solvent (physiological ionic strength) and membrane.

Molecular system

Starting structure: 7RYCPDB 7RYC(opens in a new tab)
Force field: Amber ff14SBTIP3P
Engine: GROMACS 2020.1
Method: Classical MD
Ensemble: NPT
Temperature: 304 K
Timestep: 2 fs
Frames: 30,003
Composition: Molecules of interest
ProteinProtein · 2 chains5,242 atoms325 residues
LipidsLipid29,744 atoms256 residues
OtherOther16 atoms
Total
Box dimensions: Triclinic
a9.208nm
b9.378nm
c12.509nm

Sequences

Sequence 1Protein · 9 residues

XYIQNCPLG

Sequence 2Protein · 316 residues

GPPRRNEALA RVEVAVLCLI LLLALSGNAC VLLALRTTRQ KHSRLFFFMK HLSIADLVVA VFQVLPQLLW DITFRFYGPD LLCRLVKYLQ VVGMFASTYL LLLMSLDRCL AICQPLRSLR RRTDRLAVLA TWLGCLVASA PQVHIFSLRE VADGVFDCWA VFIQPWGPKA YITWITLAVY IVPVIVLAAC YGLISFKIWQ NLRLKTAAAA AAEAPEGAAA GDGGRVALAR VSSVKLISKA KIRTVKMTFI IVLAFIVCWT PFFFVQMWSV WDANAPKEAS AFIIVMLLAS LNSCCNPWIY MLFTGHLFHE LVQRFX

Run	Outputs
OTRe replica 1	Trajectory Analyses
OTRe replica 2	Trajectory Analyses
OTRe replica 3	Trajectory Analyses

Files

37 files · 15.5 GB

All files15.5 GB

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Acknowledgements

F.M. was supported by the Italian Ministry of Education, University and Research (RFO grant 2024) and by Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP). S.A.S. was supported by a Study Grants for the Preparation of the Thesis Abroad awarded by the Department of Pharmacy and Biotechnology of the University of Bologna. The authors gratefully acknowledge the computing time provided to them at the NHR Center NHR4CES at RWTH Aachen University (project number p0020569). This is funded by the Federal Ministry of Research, Technology and Space, and the state governments participating on the basis of the resolutions of the GWK for national high-performance computing at universities (www.nhr-verein.de/unsere-partner).