Dataset Open Access

Umbrella sampling data of AuNP interacting with a PC bilayer

Heikkilä, Elena; Martinez-Seara, Hector; Gurtovenko, Andrey A.; Javanainen, Matti; Häkkinen, Hannu; Vattulainen, Ilpo; Akola, Jaakko

Files in Gromacs (v4.6) format used to generate the PMF profile shown in Fig. 3 in [1].

The nanoparticle is pulled to the EC leaflet in the 'genstart' simulations. The initial structures for the umbrella sampling windows are extracted from this trajectory. The files obtained from umbrella sampling windows are named 'pullX.*', where X is the distance between the centers of mass of the AuNP and the EC leaflet phosphori. Trajectories (.xtc) are saved every 100ps. Additionally, the initial and final structures (.gro), the run input files (.tpr), energy files (.edr), log files (.log), checkpoint files (.cpt), simulation parameter files (.mdp), and the files generated by the pull code (pull forces and pull distances, .xvg) are given for each umbrella window. Additionally, an index file (index.ndx) and a topology file (topol.top) common for all systems is provided. TOP.tar contains the molecule definitions (.itp). 'pullf-files.dat' and 'tpr-files.dat' are used by g_wham to extract the profile shown in Fig. 3 (except for the choice of the zero level) by 'g_wham -it tpr-files.dat -if pullf-files.dat -b 40000 -nBootstrap 100'

[1] Heikkilä et al., Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations, J. Phys. Chem. C, 2014, 118 (20), pp 11131–11141, DOI: 10.1021/jp5024026

Name Size
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3.5 MB Download
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genframes.log
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4.3 MB Download
genframes.xtc
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532.1 MB Download
index.ndx
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2.1 MB Download
pull10.cpt
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3.5 MB Download
pull10.edr
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4.4 MB Download
pull10.log
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pull10.mdp
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9.6 kB Download
pull10.tpr
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4.3 MB Download
pull10.xtc
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pull12.edr
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5.6 MB Download
pull12.log
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9.6 kB Download
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pull14.log
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md5:0c1d10a659099ebc7623eafe0e8526a3
6.5 MB Download
start28.gro
md5:99bf4854f25573659102889e05bd8833
6.5 MB Download
start30.gro
md5:18c1caf2d9a891a0f026fb1b2cdf3e47
6.5 MB Download
start32.gro
md5:08db6171542ecde5d343d602410311b7
6.5 MB Download
start34.gro
md5:44bba0bde2235662df8407f7f2fa3fdd
6.5 MB Download
start36.gro
md5:6a94b4a3afdecf7a1a05bf69927238db
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start38.gro
md5:3b20600348969e082f23af93a489324f
6.5 MB Download
start40.gro
md5:d201372fe6c4089a89783b20485fee57
6.5 MB Download
start42.gro
md5:111af08ee9be3ad8dcd8a89062f8b219
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start44.gro
md5:725fd6b5fba025c1796a9600d1162897
6.5 MB Download
start46.gro
md5:34a6537c29d81d911b8489e4b4f106ee
6.5 MB Download
start48.gro
md5:55abcbc6b74fd5487c5880e3299bf3a3
6.5 MB Download
start50.gro
md5:97eb116fbb8ef7464c156e6b578a41cf
6.5 MB Download
start6.gro
md5:25ee6c064b6667ef82d77ccf4d7bd511
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start8.gro
md5:040ecb7bb006b2df9b5f9096d90c0361
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TOP.tar
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topol.top
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tpr-files.dat
md5:f1c40a378d50d888eea92d2f81507879
251 Bytes Download

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