Zachary A. Levine, PhD
Postdoctoral Researcher | Shea Lab
Departments of Physics, Chemistry and Biochemistry
Materials Research Laboratory
University of California, Santa Barbara
Downloads


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Description: CHARMM36 DOPC system containing 648 lipids and 21,681 TIP3P water molecules (~33 waters/lipid). Ready to simulate with GROMACS.

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Description: OPLS/Berger POPC system containing 128 lipids and 9,006 SPC water molecules (~70 waters/lipid). Ready to simulate with GROMACS.

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Description: 2014 Annual Biophysical Society Meeting Poster

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Description: 2013 Annual Biophysical Society Meeting Poster

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Description: 2012 Annual Biophysical Society Meeting Poster

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Description: 2011 Annual Biophysical Society Meeting Poster

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Description: 2010 Annual Gordon Research Conference in Bioelectrochemistry Poster

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Description: 2010 Annual Biophysical Society Meeting Poster

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Description: 2010 Annual Bioelectromagnetic Society Meeting Poster

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Description: 2009 Annual Biophysical Society Meeting Poster.

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Description: A Perl script which draws acceleration vectors in VMD from a GROMACS .gro file.

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Description: A Perl script which quickly calculates the area per lipid from a GROMACS energy.xvg file.

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Description: A Perl script which resizes and pastes two .gro systems together into a single file.

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Description: A Perl script which reads in all .gro files in a directory and generates the anode and cathode z-dipole moments.

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Description: A Perl script which calculates the cutoff z dimension between bulk and interface water in a .gro file based on a cutoff of 80% bulk water density. Requires installation of GROMACS. Used in many other scripts as a dependency.

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Description: A batch file for converting DOPC lipids to DOPS lipids.

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Description: A script which identifies which waters are bulk water.

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Description: A Perl script which adds additional bulk water to the top and bottom of an existing .gro system.

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Description: A Perl script which transforms the geometry of .gro lipids. Required as a dependency for any PC->PS scripts.

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Description: A Perl script which holds a molecule in place by freezing the surrounding hydrating waters.

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Description: A Perl script which reads in all .gro files in a directory and generates a MATLAB graphic which displays three-dimensional dipole moments.

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Description: A perl script to convert PLPC lipids to oxidized PLPC.

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Description: A Perl script which calculates electropore radius [MPI][Deprecated].

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Description: A Perl script which calculates electropore radius [SeriaI][Current].

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Description: A script to calculate charge density values per unit time.

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Description: A script to calculate electric field values per unit time.

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Description: A script to calculate electric potential values per unit time.

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Description: A script to create bulk water and interface water atom groups in GROMACS's make_ndx function.

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Description: A script to cut out water from a .gro file based on two cutoff planes.

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Description: A Perl script to identify the pore creation times from .gro files after electroporation occurs. [requires the file below as a dependency]

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Description: A dependency file for the pore creation time routine listed above.

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Description: A Perl script to identify the pore annihilation times from .gro files after electropores dissipate. [requires the file below as a dependency]

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Description: A dependency file for the pore annihilation time routine listed above.

Zachary A. Levine |