Parashara Shamaprasad's repositories
analysis
Analysis scripts for molecular dynamics simulations of stratum corneum lipid multilayers.
cg_bond_calculator
Calculates bonded interactions from atomistic-to-CG mapped trajectories
cg_mapping
Mapping atomistic systems to coarse-grained systems
mbuild_bilayer
Bilayer builder recipe for mBuild.
antefoyer
Antechamber plugin to foyer and support for the GAFF forcefield
bayesian-stats-modelling-tutorial
How to do Bayesian statistical modelling using numpy and PyMC3
clustering
Cluster analysis tool for heterogenous lipid membranes.
ele
A lightweight package with the periodic table of the elements
example-assignment
An example assignment
example-notebooks
Example Analytic Notebooks Created for BigData and SmartCities Class
fast_wrap
A fast script to wrap atoms or molecules into a simulation box using MDTraj as a backend.
forcefield-utilities
MISC Utilities for MoSDeF Forcefields conversion
foyer
A package for atom-typing as well as applying and disseminating forcefields
glotzerlab-software
Docker image for Glotzer Lab software
gmso
Flexible storage of chemical topology for molecular simulation
gmso-examples
Demonstrating GMSO as a backend for preparing molecular simulation
hoomd-blue
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
lammps
Public development project of the LAMMPS MD software package
lipids
My CG lipids
mbuild
A hierarchical, component based molecule builder
McCabeGroup
McCabe lab repository for ceramide and phospholipid systems
mdtraj
A modern, open library for the analysis of molecular dynamics trajectories
mosdef_cassandra
MoSDeF compatible wrapper for Cassandra Monte Carlo code
msibi
A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)
reverse_mapping
Reverse mapping scheme for multi-scale molecular dynamics. Converts coarse-grained systems to the atomistic level.
Scipy2020-MoSDeF
MoSDeF Poster for Scipy2020
true_lipids
Biological simulation workflow for the TRUE paper {doi}