POPC with varying amounts of cholesterol, 450 mM of CaCl_2. Charmm36 with default Charmm ions
<p>Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 450 mM of CaCl_2 performed at 310 K. The POPC bilayer consists of 200 lipids (100 per leaflet) and on top of that there is 0 (0%), 22 (10%), 50 (20%), or 86 (30%) of cholesterol. The Charmm36 model [1,2] is employed for lipids, the Charmm compatible variant of the tip3p model for water, and the default Charmm ion parameters (type CAL) for CaCl_2.</p> <p>The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml .<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 2 µs long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), energy output file (.edr), and binary run input files (for Gromacs 5.0->) (.tpr) are provided for each system. The common simulation parameter file (.mdp) is also provided.<br> ––––––––––––––––––––––––––––––––––––––––––––––––––––––<br> [1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types. Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor, The Journal of Physical Chemistry B 2010 114 (23), 7830–7843, DOI: 10.1021/jp101759q</p> <p>[2] Update of the Cholesterol Force Field Parameters in CHARMM. Joseph B. Lim, Brent Rogaski, and Jeffery B. Klauda, The Journal of Physical Chemistry B 2012 116 (1), 203–210, DOI: 10.1021/jp207925m</p>
ShareScore
32/100
Overall dataset sharing score
Score breakdown
These five areas show where the dataset supports — or may limit — practical reuse.
- Stewardship
- 4
- Harmonization
- 4
- Access
- 16
- Reuse readiness
- 8
- Engagement
- 0
Dataset details
- Repository
- zenodo
- Published
- January 23, 2017
- License
- cc-by-4.0
- DOI
- 10.5281/zenodo.259365
Scored with release 0.9.0
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