Dataset Open Access

Large POPC monolayer simulations with Charmm36+OPC @ 298 K

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/ .

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

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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