Dataset Open Access

POPC @ 310K, varying amounts of NaCl. Model by Maciejewski and Rog

Javanainen, Matti; Tynkkynen, Joona

Input parameter files and parts of the resulting trajectories for a POPC bilayer simulation with varying amounts of NaCl. The systems contain 100, 200, 300 or 400mM NaCl. The force field is an extension to the OPLS-based force field by the same authors [1]. The data for the salt-free system is available at http://dx.doi.org/10.5281/zenodo.13498

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Files:

XXmM_50ns_100ps.xtc – XX mM NaCl; The last 50 ns of a 90 ns long simulation (40 ns discarded from the beginning). Data saved every 100 ps.

XX.tpr – XX mM NaCl. The run input file for Gromacs versions 4.5 and above. 

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This data is used in the project "Matching lipid force fields with NMR data", see: http://nmrlipids.blogspot.fi and referred to in the blog as 'MacRog'

[1] Maciejewski, A., Pasenkiewicz-Gierula, M., Cramariuc, O., Vattulainen, I., and Rog, T. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration. The Journal of Physical Chemistry B 118, 4571–4581 (2014). DOI: 10.1021/jp5016627

Files (614.7 MB)
Name Size
100.tpr md5:1f465dde3a920627d55804f5b129c6b4 2.4 MB Download
100mM_50ns_100ps.xtc md5:6f2a4bf619a3a24cc820c18edf932103 151.9 MB Download
200.tpr md5:df49dbfce96ab26badf619859f52060f 2.4 MB Download
200mM_50ns_100ps.xtc md5:26495e163ababf07e6c664bd119ac602 151.7 MB Download
300.tpr md5:4077a8b9bafb52780e2105ad56e5590f 2.4 MB Download
300mM_50ns_100ps.xtc md5:a7d9ea0fe0fa186092743ef4bab1c94b 150.3 MB Download
400.tpr md5:188ba6a4664fc6014cd7803999fd0559 2.4 MB Download
400mM_50ns_100ps.xtc md5:93927d284ccbbed276c58db8d4ad7d53 151.4 MB Download

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