Dataset Open Access

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

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 ***

This is a correction to an earlier dataset simulated with some missing dihedrals, see: DOI: 10.5281/zenodo.61649

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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. 

UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.

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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

 

[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 (5.2 GB)
Name Size
chol0.edr
md5:e195c66512fd220730585a69d414286d
31.2 MB Download
chol0.gro
md5:de691db00ccc75eb4cc2659997dc98c6
3.7 MB Download
chol0.ndx
md5:a054230c11ff4c0d38a20385381d1014
1.3 MB Download
chol0.top
md5:92016a55a5c8f2e8eed000b4bc9a0813
146 Bytes Download
chol0.tpr
md5:5cbd58ce79e96e1cfcb42215a3af234b
1.8 MB Download
chol0.xtc
md5:954ab17e0385c6bef4f5b60d8e220e97
199.2 MB Download
chol0_500ns.cpt
md5:46e5c9f081c9a0f080fff578e9be64f6
1.3 MB Download
chol0_500ns.xtc
md5:7b5c997e5ae0ac22c160671e11e8bb25
995.1 MB Download
chol10.edr
md5:df226f5343e03bfe2297d575fd81c53c
31.2 MB Download
chol10.gro
md5:0668733fcb5a08778a252c89329632f3
3.8 MB Download
chol10.ndx
md5:593f0567a8b4dd9a8e24d4230e855bbc
1.3 MB Download
chol10.top
md5:a5c28be711003edae662778efbc74422
187 Bytes Download
chol10.tpr
md5:efb76b3238320d95adb5ea6486694572
1.8 MB Download
chol10.xtc
md5:3fd5ee3a8815a856741e14da4e12cbae
205.3 MB Download
chol10_500ns.cpt
md5:66ccc4d1290e7a3534df9794c10dcb01
1.3 MB Download
chol10_500ns.xtc
md5:5a0fa62f3efa7a9037dc6b75c750a85f
1.0 GB Download
chol20.edr
md5:be6eecd2bbee7680db993b8bb85d14df
31.2 MB Download
chol20.gro
md5:479aefc0ee0d6dbf77cebdb027e27aaf
4.0 MB Download
chol20.ndx
md5:3152b8e302fc9631738343908b8072bd
1.4 MB Download
chol20.top
md5:edd88e49cddddc146c8e1e95a06f1ad0
187 Bytes Download
chol20.tpr
md5:a8fc836c726794ec7efb4926be42867e
1.9 MB Download
chol20.xtc
md5:8d1ec1a27eff11c8714737f181f6f5f8
213.8 MB Download
chol20_500ns.cpt
md5:1da6ab1e23407a01b717f3b3fe8f836f
1.4 MB Download
chol20_500ns.xtc
md5:a03bd1d3cffd09064ae7b35ed66129b5
1.1 GB Download
chol30.edr
md5:c47ce43e215633542df396cd13b14345
31.2 MB Download
chol30.gro
md5:080e2e5649764dfd80df9b5f16a5fd41
4.2 MB Download
chol30.ndx
md5:4f23c039de7518bf88c5ec5e148436bf
1.4 MB Download
chol30.top
md5:c1d29b98191608457612d0247561e75d
188 Bytes Download
chol30.tpr
md5:c0a97004d05c3ed9d6aee0abbc7431fe
2.0 MB Download
chol30.xtc
md5:d73840fbec11136de0f51256abf89001
224.9 MB Download
chol30_500ns.cpt
md5:9c74bdb00d041fe60ab674011f54363a
1.4 MB Download
chol30_500ns.xtc
md5:04e2afa2c4a0b5285339454dd4b782d7
1.1 GB Download
md.mdp
md5:58558e3dcc25460ff5ddb995f0ba9a91
1.1 kB Download
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