Dataset Open Access

POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. *OBSOLETE*

Javanainen, Matti

A POPC bilayer consisting of 200 lipids (100 per leaflet) 
is simulated in the presence of 0% (0 molecules), 10 %
(22 molecules), 20 % (50 molecules), or 30 % (86 molecules)
of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.

The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org

 

*** IMPORTANT ***

These simulations were performed using an erroneous charmm36.itp file provided by version 1.7 of CHARMM-GUI, as stated in  http://www.charmm-gui.org/?doc=log : "The multiplicity (of dihedral parameters) issue in GROMACS inputs; this issue affects the systems generated from August 21th 2015 to December 9th 2015." Due to the bad .itp, the deuterium order parameters of C2, as well as the glycerol group, show strange behavior. The systems simulated with the correct itp file can be accessed at: DOI: 10.5281/zenodo.159759.

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The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. 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. 

––––––––––––––––––––––––––––––––––––––––––––––––––––––

[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] 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 (996.9 MB)
Name Size
chol0.edr
md5:15b6a348a51975a16577ef809b33a9f8
31.2 MB Download
chol0.gro
md5:a1ac22db043b23108dcdcb5c29340282
3.7 MB Download
chol0.ndx
md5:a054230c11ff4c0d38a20385381d1014
1.3 MB Download
chol0.top
md5:06f15a09f0947eb4f1a79f991abdef99
146 Bytes Download
chol0.tpr
md5:844bc2b9f325915c38b1e970df4bd8f3
1.8 MB Download
chol0.xtc
md5:030e00ca4ed27915ab13d6efc205cf4e
199.2 MB Download
chol10.edr
md5:0635309d4913d677c6d9563e95f5af6f
31.2 MB Download
chol10.gro
md5:45285d4c872b8e40a2501f2fc0742ec2
3.8 MB Download
chol10.ndx
md5:593f0567a8b4dd9a8e24d4230e855bbc
1.3 MB Download
chol10.top
md5:c75f9cae779c0660f14dc292e3b195bc
187 Bytes Download
chol10.tpr
md5:5e7aabbe6993cf337262757143f3718b
1.8 MB Download
chol10.xtc
md5:8f18b4e8a5a9d299b39f03dce8c7c5e3
205.3 MB Download
chol20.edr
md5:364df7462da5ae824f48876b048171d9
31.2 MB Download
chol20.gro
md5:9986f4a9109a3eae7197280fef2981fd
4.0 MB Download
chol20.ndx
md5:3152b8e302fc9631738343908b8072bd
1.4 MB Download
chol20.top
md5:2f3bb36b5ac9ef2615684057d74109c7
187 Bytes Download
chol20.tpr
md5:fc9721967e68b89e01aa60fed54a14e4
1.9 MB Download
chol20.xtc
md5:e35047d0e8df1d23eb249f03818b90dd
214.2 MB Download
chol30.edr
md5:af711e47fd251154882502774e0dee0b
31.2 MB Download
chol30.gro
md5:3b9af3b7d78a9add9eed49dd2ae6e6c0
4.2 MB Download
chol30.ndx
md5:4f23c039de7518bf88c5ec5e148436bf
1.4 MB Download
chol30.top
md5:853ddd682463c3438e3df81ad9ff8d50
188 Bytes Download
chol30.tpr
md5:1bf30f42e64233b73375c552bdc2e049
2.0 MB Download
chol30.xtc
md5:5c8430a2a4a76d03f976e73ca4eaa3c4
224.9 MB Download
md.mdp
md5:38a4694b6c335102723669a94ce3022c
1.2 kB Download
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