Title: POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. *OBSOLETE*

Type Dataset Javanainen, Matti (2016): POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field. *OBSOLETE*. Zenodo. Dataset. https://zenodo.org/record/61649

Author: Javanainen, Matti (TUT) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

A POPC bilayer consisting of 200 lipids (100 per leaflet)  is simulated in the presence of 0% (0 molecules), 10 % (22 molecules), 20 % (50 molecules), or 30 % (86 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.

The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org

*** IMPORTANT ***

These simulations were performed using an erroneous charmm36.itp file provided by version 1.7 of CHARMM-GUI, as stated in  http://www.charmm-gui.org/?doc=log : "The multiplicity (of dihedral parameters) issue in GROMACS inputs; this issue affects the systems generated from August 21th 2015 to December 9th 2015." Due to the bad .itp, the deuterium order parameters of C2, as well as the glycerol group, show strange behavior. The systems simulated with the correct itp file can be accessed at: DOI: 10.5281/zenodo.159759.

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The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. 

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[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites,  Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor

The Journal of Physical Chemistry B 2010 114 (23), 7830-7843

DOI: 10.1021/jp101759q

[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im

Journal of Chemical Theory and Computation 2016 12 (1), 405-413

DOI: 10.1021/acs.jctc.5b00935

More information

• DOI: 10.5281/zenodo.61649

Dates

• Publication date: 2016
• Issued: September 05, 2016

Rights

• https://creativecommons.org/publicdomain/zero/1.0/legalcode Creative Commons Zero v1.0 Universal
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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