Constant pH MD of small HER2-siRNA LNP at pH 12 (processed, without solvent)

Kazi Amirul Hossain,Mariana Valério,Pedro Medina,Paulo C. T. Souza,Modesto Orozco

Created 20 Oct 2026Updated 20 Oct 2026

MD-A00C75

Description

All-atom constant pH MD (GROMACS CpHMD lambda dynamics) of the simplified self-assembled HER2-siRNA lipid nanoparticle (siRNA, titratable MC3 ionizable lipids, DSPC, cholesterol, DMG-PEG) in explicit water at pH 12. Two replicas. Solvent-stripped trajectories with titrating MC3 lipids renamed according to their protonation state.

Molecular system

Program: GROMACS 2021

Sequences

Sequence 1Nucleic acid · 10 residues

CUCACAGAGA

Sequence 2Nucleic acid · 10 residues

UCUCUGUGAG

Run	Outputs
r_1/pH_12.00_r_1	Trajectory Analyses
r_2/pH_12.00_r_2	Trajectory Analyses

Files

17 files · 163 MB

All files163 MB

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

Funded by Instituto de Salud Carlos III (PI18/01964; XNA-Hub Project), Spanish Ministry of Science, Innovation and Universities (FPU19/05307, PDI2021-122478NB-I00, PCI2022-134976-2), CDTI EndRam Project (PLEC2024-011123), Generalitat de Catalunya AGAUR (2021SGR0086), CNRS and Sanofi; computing resources from EuroHPC (EHPC-EXT-2024E01-045, BSC), GENCI (IDRIS, CINES, TGCC) and PSMN / Centre Blaise Pascal (ENS de Lyon).