Dataset Open Access

POPC @ 310K, Model by Ulmschneider and Ulmschneider

Javanainen, Matti

Files required for a simulation of a POPC bilayer and the resulting trajectories. The POPC model is that by Ulmschneider and Ulmschneider [1]. The structure and topology files are downloaded from Lipidbook [2]. The files (xtc and mdp) with '_dc' suffix are simulated with dispersion correction applied to both energy and pressure whereas the files without this suffix do not use this correction.

This data is used in the project "Matching lipid force fields with NMR data", see: http://nmrlipids.blogspot.fi 

[1] J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813

[2] http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html

Files (1.2 GB)
Name Size
ffbonded.itp md5:1128303a9b1adbdc13e772e45c1e4339 220.7 kB Download
ffnonbonded.itp md5:0ba729abc03d0a972d99522242dc447f 65.6 kB Download
forcefield.itp md5:883604eae7c155e8ae3c76ecb731415f 888 Bytes Download
gbsa.itp md5:6575f1185a012d3c6c480fe657fd8dc1 4.5 kB Download
index.ndx md5:8d97253e4bc70a958f72e56add042b38 306.6 kB Download
md.mdp md5:4f03bce678222b4666c740820e7546c0 982 Bytes Download
md.xtc md5:d6f26060ce0c83e14463805c55554593 610.3 MB Download
md_dc.mdp md5:0060e7ed352ec4bf24b359ac49bd862a 1.0 kB Download
md_dc.xtc md5:d1ae39d24f5f22d8111da01e7e09be0b 610.3 MB Download
mdout.mdp md5:6095ad3f1fa2140447655378dff87c48 10.4 kB Download
opls-ua-lipid-atomtypes.itp md5:771aae352624b330626e33c8695949a9 2.4 kB Download
popc_opls.itp md5:fd3fbda2953e00e4a3f9e274502c236e 26.9 kB Download
start.gro md5:89da19fe0f197b1bc0b221f05783bec6 748.9 kB Download
topol.top md5:827b8b9da983ed9fb98060f218a6b48f 228 Bytes Download

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