Title: Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014

Type Dataset Claire Loison (2015): Hydrated DPPC, MD simulation trajectory and related files for UA charmm36 model by Lee et al 2014. Zenodo. Dataset. https://zenodo.org/record/16978

Author: Claire Loison (CNRS, Université de Lyon) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

MD simulation files

72 hydrated DPPC  + 2189 water TIP3P 

NPgT

P=1atm, gamma=0, T=323K (liquid crystalline phase)

20 ns equilibration (not here)

50 ns trajectory (dcd file)

Model : Lee S, Tran A, Allsopp M, Lim JB, Hénin J, Klauda JB. CHARMM36 United Atom Chain Model for Lipids and Surfactants. J Phys Chem B. 2014;118(2):547-556. doi:10.1021/jp410344g.

---- * bilayer-72DPPC-c36-AU.psf : NAMD2.10 structure file Obtained with psfgen utility, using

1) topology from Lee et al.  2014

2) positions from J. Klauda.

http://terpconnect.umd.edu/~jbklauda/research/download.html

----

* dppc_c36_AU.equil.2.dcd : trajectory file of 2635 frames every 20 ps.

--- * measure_SCD_heads.tcl : file used to measure order parameters for the head hydrogens using vmd-1.9

---

*namd_input.tar files usefull to launch the simulations using NAMD(2.10).  

More information

• DOI: 10.5281/zenodo.16978

Subjects

• NAMD, DPPC, MD simulations, lipid bilayers

Dates

• Publication date: 2015
• Issued: April 20, 2015

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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