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All-atom simulation of DOPC with 20 mol% cholesterol

Research datakeyboard_double_arrow_right Dataset 09 May 2025Publisher:ZenodoFunded by:NSF | IMR-MIP DANSE - Distribut..., NSF | MRI: Acquisition of a Nex..., NIH | MEMBRANE BASIS OF VISUAL ... +8 projects

Authors: Doktorova, Milka; Kheashvili, George;

doi: 10.5281/zenodo.15370304 , 10.5281/zenodo.15374489 , 10.5281/zenodo.15374488 , 10.5281/zenodo.15370303

All-atom simulation of DOPC with 20 mol% cholesterol

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Abstract

Fully hydrated all-atom bilayer of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with 20 mol% cholesterol (Chol). The bilayer was constructed with CHARMM-GUI and has 100 lipids per leaflet and no added salt ions. After equilibration in NAMD following CHARMM-GUI's 7-step protocol, the system was simulated at 25C (298K) with OpenMM for 2 microseconds. Uploaded are the structure file (.psf), trajectory centered on the bilayer midplane with output frequency 40 ps (50,200 frames total, .dcd) and a sample OpenMM input parameter file (.txt).

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Stockholm University
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NSF| IMR-MIP DANSE - Distributed Data Analysis for Neutron Scattering Experiments - CNST, NSF| MRI: Acquisition of a Next Generation Small-Angle X-ray Scattering System for Nanoscale Characterization and Development of Advanced Functional Materials, NIH| MEMBRANE BASIS OF VISUAL EXCITATION, NSF| Essential Role of Water and Lipids in G-Protein-Coupled Receptor Chemistry

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