Dataset Open Access

Large POPC monolayer simulations with Charmm36+OPC @ 298 K (Part 1/2)

Javanainen, Matti

POPC monolayers simulated at a varying area per lipid in the NVT ensemble. The Charmm36 lipid model [1] is employed together with the 4-point OPC water model [2]. Each system contains two monolayers with 256 lipids each. These monolayers are separated by a water slab, and surrounded by vacuum. 

The number in the filename corresponds to the area per lipid in Ångströms. The starting structures were generated by setting up a system with an area per lipid of 50 Å^2, followed by a simulation during which the monolayer area was expanded using PLUMED. 

All trajectories, 100 ns long, are simulated with Gromacs 5.0.x [3] using the default Charmm36 monolayer simulations parameters given in the mdp file. Topology (.top) and index files are also common for all simulations. The topologies (.itp) for the lipids can be obtained from Charmm-GUI and for the OPC water model from https://bioinformatics.cs.vt.edu/~izadi/ .

Part 2 of this upload is available at: https://doi.org/10.5281/zenodo.838633

[1] DOI: 10.1021/jp101759q
[2] DOI: 10.1021/jz501780a
[3] DOI: 10.1016/j.softx.2015.06.001

Files (12.0 GB)
Name Size
index.ndx md5:158fba5af13ca63e63eb3af750b3ceed 5.5 MB Download
mono.mdp md5:ad9d0b4dacb0c6b4b53a5a3d156e7b8d 1.2 kB Download
POPC-298K-102.cpt md5:0190ae93276fe802784acc830e33de6a 5.6 MB Download
POPC-298K-102.edr md5:f157cb2d7bbf39d78c11cb1c47e006ba 54.0 MB Download
POPC-298K-102.gro md5:d259ae5cbe256596f672ac73ca956450 16.2 MB Download
POPC-298K-102.tpr md5:3817920b0b3d7d938708a95baf6ad707 7.5 MB Download
POPC-298K-102.xtc md5:4017e2ac20618564b5e9f3e136eb2287 841.3 MB Download
POPC-298K-110.cpt md5:83c81aee31002d7a16a06ffaa94e40ae 5.6 MB Download
POPC-298K-110.edr md5:94ffbc96ea9928df2fb651c4a2546c49 54.0 MB Download
POPC-298K-110.gro md5:5619d6f0bc72921fcdf78e979ee85dc7 16.2 MB Download
POPC-298K-110.tpr md5:f30ea858dcd808cf5e13e9c99b7ef381 7.5 MB Download
POPC-298K-110.xtc md5:617e6075c7611d53a6d2968e4d107af1 841.1 MB Download
POPC-298K-118.cpt md5:c38c9be21370092e43de30c3083a2194 5.6 MB Download
POPC-298K-118.edr md5:f47d00a2adb5242187aaf053b5250945 54.0 MB Download
POPC-298K-118.gro md5:f117770119e1810351c615a2c880d352 16.2 MB Download
POPC-298K-118.tpr md5:a6f47f1923a4dcb8b5714ae04a6b0b37 7.5 MB Download
POPC-298K-118.xtc md5:03de8fa15acf44c504531b03abcdebe8 841.0 MB Download
POPC-298K-126.cpt md5:495c172dea0c1a1b59b4a033aa726ab0 5.6 MB Download
POPC-298K-126.edr md5:c5df1f68a2eb89b57a0dbe82bc05e501 54.0 MB Download
POPC-298K-126.gro md5:fd91e632d56ba647414f87db8c924ef1 16.2 MB Download
POPC-298K-126.tpr md5:cf9e30ba40186f4979159e0e2b4d6ef1 7.5 MB Download
POPC-298K-126.xtc md5:73849f013381a0fa084853add5febc5d 841.0 MB Download
POPC-298K-55.cpt md5:78c46839e693844640700ea1c7b92b14 5.6 MB Download
POPC-298K-55.edr md5:24228546fc979e3a34f66291e9150f7c 54.0 MB Download
POPC-298K-55.gro md5:e5de01a357e9e9c61b8b71495894510a 16.2 MB Download
POPC-298K-55.tpr md5:c80b3dd18154bdcbdfd9619de5b84980 7.5 MB Download
POPC-298K-55.xtc md5:707c1801b06b56c785226676ddb58799 836.7 MB Download
POPC-298K-58.cpt md5:d6ddcc6b44e24847651faafc1fe16c41 5.6 MB Download
POPC-298K-58.edr md5:4c2d7b0e3ab4112576dbfee955ce16d6 54.0 MB Download
POPC-298K-58.gro md5:c613ae08a88f6b017caa4abd5aa721e3 16.2 MB Download
POPC-298K-58.tpr md5:c045d01bf4d82aaea330d4e0bd6bd0b5 7.5 MB Download
POPC-298K-58.xtc md5:0d3c25f33e5181070b25d6aa5de760f7 836.3 MB Download
POPC-298K-61.cpt md5:73796bfa5afbe58aaab3872ee86ccb26 5.6 MB Download
POPC-298K-61.edr md5:3dbf17753d708932d82cf28dd18f752e 54.0 MB Download
POPC-298K-61.gro md5:f3d3a0f701fc3a88e060feec0ddc2080 16.2 MB Download
POPC-298K-61.tpr md5:3a0ec56e594eb173f10a846a5d8a14af 7.5 MB Download
POPC-298K-61.xtc md5:161ba45aaa394fa08facd1b4038ca692 837.0 MB Download
POPC-298K-64.cpt md5:f77a7e82099ef7f80b24ab3506c468b6 5.6 MB Download
POPC-298K-64.edr md5:30731a0e8922710fea44a1d143f566e9 54.0 MB Download
POPC-298K-64.gro md5:a45c3141fb34bc1cd7700ebe6a5fb3eb 16.2 MB Download
POPC-298K-64.tpr md5:c2d9c3edeed08cb92ef91279ebfd129b 7.5 MB Download
POPC-298K-64.xtc md5:bae536d90e2c60921a644d059b381d5d 836.4 MB Download
POPC-298K-67.cpt md5:b865dfe7c1b6fd4226bb250f54ad244e 5.6 MB Download
POPC-298K-67.edr md5:45964b4f01e0ee811fe4f1765dbbff13 54.0 MB Download
POPC-298K-67.gro md5:bb006e7b351868d72a8df71307b07966 16.2 MB Download
POPC-298K-67.tpr md5:65017314187c48db1dd3a0688fd35737 7.5 MB Download
POPC-298K-67.xtc md5:01cf7edd751529b684e44170fba372e7 835.9 MB Download
POPC-298K-70.cpt md5:29f9a1fdf902e86807e2f7264f380def 5.6 MB Download
POPC-298K-70.edr md5:6d0a1b418e4cc7081c8385ee0c3ee40a 54.0 MB Download
POPC-298K-70.gro md5:f5b8e0b63816f8027621d0f4df9a60a0 16.2 MB Download
POPC-298K-70.tpr md5:a445cc22f1b3806bb3c28dc1d3e39a9c 7.5 MB Download
POPC-298K-70.xtc md5:2a3a67e4323fc1adbe7389b3cbdf7767 836.5 MB Download
POPC-298K-78.cpt md5:2faa3f54e6fe8667a3cb6316ea75e04d 5.6 MB Download
POPC-298K-78.edr md5:13c347782f831b78c6b4172c8c8c5ab4 54.0 MB Download
POPC-298K-78.gro md5:2fd37621940b0d4be9a11b0445e10aff 16.2 MB Download
POPC-298K-78.tpr md5:8253f035d85c4654955ea27cd2072cfa 7.5 MB Download
POPC-298K-78.xtc md5:1d897a316e0b2c0421f72bfcf06715b5 839.0 MB Download
POPC-298K-86.cpt md5:9b247cadb56dbc0d93bd13678794e296 5.6 MB Download
POPC-298K-86.edr md5:790108645d674a2cbd90bc54c631ea44 54.0 MB Download
POPC-298K-86.gro md5:0727b41d0879ce2c424a81a33637d2f8 16.2 MB Download
POPC-298K-86.tpr md5:abdb3d29a34f9bfa49a0a59d4228f5fa 7.5 MB Download
POPC-298K-86.xtc md5:5b841affa65dc3d1fa9aaf3ab342ce93 841.6 MB Download
POPC-298K-94.cpt md5:604c90c6864f37a277a261300810eb57 5.6 MB Download
POPC-298K-94.edr md5:286ee2f2f615da1cabf3821726dca7a2 54.0 MB Download
POPC-298K-94.gro md5:36f4bb0e4fd3d3c04e91d50cd2abf794 16.2 MB Download
POPC-298K-94.tpr md5:b612470341696406941df510e08abf11 7.5 MB Download
POPC-298K-94.xtc md5:cc0c68292e32fc1f325d9d7b51e6c8e7 841.5 MB Download
topol.top md5:98bcb479564e88f1f3d9bd505c909192 169 Bytes Download

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