Molecular Dynamics Trajectories  Transprotein Electropore Formation

Authors: Marracino, Paolo; Bernardi, Mario; Liberti, Micaela; Signore, Federico Del; Trapani, Erika; Garate, Jose Antonio; Burnham, Christian J.; +2 Authors

doi: 10.5281/zenodo.1310976 , 10.5281/zenodo.1310975

Molecular Dynamics Trajectories Transprotein Electropore Formation

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Abstract

AQP4_MD.conf: NAMD example input file. AQP_cw_pope_wi.pdb: coordinates of AQP4 tetramer embedded in an POPC bilayer fully solvated and neutralized. AQP_cw_pope_wi.psf: topology of AQP4 tetramer embedded in an POPC bilayer fully solvated and neutralized. par_all27_prot_lipid.prm: CHARMM parameter file. z+.0.05va.5ns.dcd: Trajectory of electropore formation. z+.stat_frame1600.0.02va.46ns.dcd: Trajectory of electropore stabilization (holding potential) z+.stat_frame1700.0.02va.66ns.dcd: Trajectory of electropore stabilization (holding potential) Naming Convention: field_direction.starting_frame.potential_value(in volts/A).simulated_time.dcd To load any dcd file, load first the psf or pdb file in VMD.

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Keywords

Molecular Dynamics, human Aquaporin 4, electroporation, electric fields

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