Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Large Popc Monolayer Simulations With Charmm36+Opc @ 298 K      
dateReleased:
03-03-2017
privacy:
information not avaiable
aggregation:
instance of dataset
dateCreated:
02-27-2017
refinement:
raw
ID:
doi:10.5281/ZENODO.322830
creators:
Javanainen, Matti
availability:
available
types:
other
description:
POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum.  The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED.  All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ . [1] DOI: 10.1021/jp101759q [2] DOI: 10.1021/jz501780a [3] DOI: 10.1016/j.softx.2015.06.001
accessURL: https://doi.org/10.5281/ZENODO.322830
storedIn:
Zenodo
qualifier:
not compressed
format:
HTML
accessType:
landing page
authentication:
none
authorization:
none
abbreviation:
ZENODO
homePage: https://zenodo.org/
ID:
SCR:004129
name:
ZENODO

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.