Published January 24, 2017 | Version v1

POPC with varying amounts of cholesterol, 130 mM of NaCl. Charmm36 with default Charmm ions

Authors/Creators

  • 1. TUT

Description

Simulations of a POPC bilayer with varying amounts (0, 10, 20, and 30 mol-%) of cholesterol and 130 mM of NaCl 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 standard Charmm ion parameters for NaCl [3].

The Charmm36 force field parameters were obtained Charmm-GUI [4]. IMPORTANT: The simulations are performed with version 1.7 obtained from Charmm-GUI, and this version is known to have an issue with the multiplicity of dihedrals in Gromacs output files, see http://www.charmm-gui.org/?doc=log . 
––––––––––––––––––––––––––––––––––––––––––––––––––––––
The files are in GROMACS format and named based on the amount of cholesterol present (in %) in the corresponding simulation. Trajectories (.xtc) are 200 ns 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.
––––––––––––––––––––––––––––––––––––––––––––––––––––––
[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

[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

[3] Control of Ion Selectivity in LeuT: Two Na+ Binding Sites with Two Different Mechanisms. Sergei Y. Noskov and Benoit Roux, Journal of Molecular Biology 2008 377 (3), 804–818, DOI:10.1016/j.jmb.2008.01.015

[4] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, 
Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im, Journal of Chemical Theory and Computation 2016 12 (1), 405-413, DOI: 10.1021/acs.jctc.5b00935

Files

Files (1.7 GB)

Name Size
md5:b44ff569eeb7fd00fcd34ee18ec49348
1.2 kB Download
md5:f560dd7ec80e1f170c536697fb1323d8
513.4 kB Download
md5:6bcc39e584e9b4ecb12c184464596a06
3.7 MB Download
md5:b2ae9491b4f734472fecf727f79fb2d5
1.3 MB Download
md5:1488d748cc21768452feb5bc0db63ea2
231 Bytes Download
md5:02f544723a04f93437247328a0f01984
1.8 MB Download
md5:3b57d9b3d4b72ffcdf58c57b0bc2f86d
398.6 MB Download
md5:c901dc87768c9c481c7b9c32b343ca77
513.4 kB Download
md5:10bb5f950ca217b99fbd456686ecd5a7
3.8 MB Download
md5:8e4def799e62bc7449e9d539de798b90
1.3 MB Download
md5:56b4a6ca74b43a34e7655b394e476178
272 Bytes Download
md5:772c93406825aed969d60b1de690c1fb
1.8 MB Download
md5:65893b526ae8a2d009e948d8256ea6dc
410.8 MB Download
md5:629c42326c7107134deb826d790b35e2
513.4 kB Download
md5:7e3ebb43490c376c152d4795e41c8919
4.0 MB Download
md5:e3eecba473d2ba31029ede95dc643258
1.4 MB Download
md5:c926a3c269c258196ea435fbe75526a9
272 Bytes Download
md5:51382e7cef021b9c13f04831998abb23
1.9 MB Download
md5:7d75b20a59fe5d8d33cc2178061c42cf
429.0 MB Download
md5:c54ede9e966af260fc3041dcdf19f2b9
513.4 kB Download
md5:76bf864ab434d097a631b58322c5eb04
4.2 MB Download
md5:f867e47514e36d9a429f7e1a57c583d9
1.4 MB Download
md5:4478508e72629743e4cc67db8bd34271
272 Bytes Download
md5:6d97b699d7d4b553c6bad811b6eb21db
2.0 MB Download
md5:5bebcbcb156fdf04897111e6196965f4
450.1 MB Download