orbeckst
I lead a computational research group in the Department of Physics at Arizona State University (@Becksteinlab) and am a co-founder of @MDAnalysis.
Arizona State UniversityTempe, AZ, USA
Pinned Repositories
alchemlyb
the simple alchemistry library
GromacsWrapper
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
MDPOW
Calculation of water/solvent partition coefficients with Gromacs.
GridDataFormats
GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.
mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
pmda
Parallel algorithms for MDAnalysis
g_count
g_count and g_flux are simple Gromacs tools that are primarily useful to characterize movement of water inside a cylindrical region. This can be the pore of an ion channel or a carbon nanotube. g_count returns statistics about how many atoms of a certain type (for instance, water oxygens) occupied the region of interest. g_flux calculates the flux through a cylindrical region. g_zcoord is a dumb piece of code that just prints z-coordinates of atoms in a cylindrical region; it should be easy enough to add additional functionality. g_flux is more sophisticated than g_count and gives more detailed information but you are encouraged to check that the reported results agree with what you can see in your system. For instance, get the indices of translocating particles and then track them in a trajectory viewer such as VMD. Detailed documentation can be found in the help functions for each program (run it with -h). Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis. When you use g_flux/g_count please cite * O. Beckstein and M. S. P. Sansom, The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores, Phys. Biol. 1 (2004), 42–52. doi:10.1088/1478-3967/1/1/005
gridcount
DEPRECATED and UNSUPPORTED. gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles").
RecSQL
RecSQL is a hack that allows one to load table-like data records into an in-memory sqlite database for quick and dirty analysis via SQL. The SQLarray class has additional SQL functions such as sqrt or histogram defined. SQL tables can always be returned as numpy record arrays so that data can be easily handled in other packages such as numpy or plotted via matplotlib. Selections produce new SQLarray objects.
Tutorials
tutorials for MD etc
orbeckst's Repositories
orbeckst/g_count
g_count and g_flux are simple Gromacs tools that are primarily useful to characterize movement of water inside a cylindrical region. This can be the pore of an ion channel or a carbon nanotube. g_count returns statistics about how many atoms of a certain type (for instance, water oxygens) occupied the region of interest. g_flux calculates the flux through a cylindrical region. g_zcoord is a dumb piece of code that just prints z-coordinates of atoms in a cylindrical region; it should be easy enough to add additional functionality. g_flux is more sophisticated than g_count and gives more detailed information but you are encouraged to check that the reported results agree with what you can see in your system. For instance, get the indices of translocating particles and then track them in a trajectory viewer such as VMD. Detailed documentation can be found in the help functions for each program (run it with -h). Background information (slighly outdated for the current g_count-gmx4.5 release) can be found in the appendix (pdf) of my thesis. When you use g_flux/g_count please cite * O. Beckstein and M. S. P. Sansom, The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores, Phys. Biol. 1 (2004), 42–52. doi:10.1088/1478-3967/1/1/005
orbeckst/RecSQL
RecSQL is a hack that allows one to load table-like data records into an in-memory sqlite database for quick and dirty analysis via SQL. The SQLarray class has additional SQL functions such as sqrt or histogram defined. SQL tables can always be returned as numpy record arrays so that data can be easily handled in other packages such as numpy or plotted via matplotlib. Selections produce new SQLarray objects.
orbeckst/gridcount
DEPRECATED and UNSUPPORTED. gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles").
orbeckst/Tutorials
tutorials for MD etc
orbeckst/AdK_analysis
Old Python scripts and libraries to analyze the simulations in Beckstein et al, J Mol Biol 394 (2009), 160.
orbeckst/pgeom
Generating atomistic models of ion channel pores as used in O. Beckstein, Philip C. Biggin and Mark S. P. Sansom, A hydrophobic gating mechanism for nanopores, J. Phys. Chem. B 105 (2001), 12902-12905 and later publications.
orbeckst/MDAnalysis.github.io
MDAnalysis home page mdanalysis.org as GitHub pages.
orbeckst/orbeckst.github.com
Personal Github page
orbeckst/alchemlyb-feedstock
A conda-smithy repository for alchemlyb.
orbeckst/bioconda-recipes
Conda recipes for the bioconda channel.
orbeckst/CpHMD-Analysis
Jack Henderson's CHARMM CpHMD analysis scripts
orbeckst/docsearch-configs
DocSearch - Configurations
orbeckst/docsearch-scraper
DocSearch - Scraper
orbeckst/duecredit
Automated collection and reporting of citations for used software/methods/datasets
orbeckst/GitHub-Classroom-Introductory-Assignment
Starter lesson for assessing GitHub Classroom use.
orbeckst/gsoc
NumFOCUS Google Summer of Code Materials
orbeckst/gsod
NumFOCUS participation information for Google Season Of Docs
orbeckst/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
orbeckst/MDAnalysisSandbox
user contributed analysis modules
orbeckst/mdanalysistests-feedstock
A conda-smithy repository for mdanalysistests.
orbeckst/mean_calculator
Workshop 2018 test repo
orbeckst/mean_demo
demo for CI
orbeckst/nep29
orbeckst/periodic-table
orbeckst/PHY494
orbeckst/PyBOL
orbeckst/Simple-SQL-Exercise
Exercise for testing SQL testing and GitHub actions.
orbeckst/solvation_analysis-feedstock
A conda-smithy repository for solvation_analysis.