Published May 9, 2016 | Version v1

POPC @ 310K, 450 mM of CaCl_2. Charmm36 with default Charmm ions

Authors/Creators

  • 1. TUT

Description

Simulations of a POPC bilayer with 450 mM of CaCl_2. 
The goal was to study the effect of salt on the order 
parameters of the lipid head group and the glycerol 
backbone for the NMRlipids project, see 
http://nmrlipids.blogspot.fi for more information.

A POPC bilayer consisting of 200 lipids (100 per leaflet) 
is simulated in the presence of 450 mM CaCl_2. The Charmm36 
model [1] 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.

The Charmm36 force field parameters were obtained from http://mackerell.umaryland.edu/charmm_ff.shtml

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The files are in GROMACS format. Trajectory (.xtc) is 
100 ns long with data saved every 100 ps. These data
were collected after 1900 ns of simulation Additionally,

the initial structure (.gro), topology (.top), index file (.ndx), 
simulation paremeter file (.mdp), binary run input file 
for GROMACS v. 5.0–> (.tpr) and the energy output file 
(.edr) are provided. 

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[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

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