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Title ID Description
Head and Neck Musculoskeletal Biomechanics neck_mechanics This project contains models, images and data for analysis of the neck musculoskeletal system. This...
How Tendon Compliance Affects the Metabolic Cost of Running metabolics_run We investigated the effect of tendon compliance on the metabolic cost of running using a full-body m...
Torso + Lower Extremity Model torso_legs This project contains an OpenSIM model file that includes a torso segment in addition to the lower e...
iAMOEBA, an Inexpensive AMOEBA Polarizable Water Model iamoeba iAMOEBA is an inexpensive and highly accurate polarizable water model. It is based on the AMOEBA mo...
OpenSim Musculoskeletal Model of a Sheep Hind Limb sheep_hind_limb The purpose of this study was to develop a musculoskeletal model of an adult sheep hind limb and inv...
A Python implementation of the multistate Bennett acceptance ratio (MBAR) pymbar pymbar has migrated to GitHub: https://github.com/choderalab/pymbar
Sam's Simulations samsim This project is intended to serve as a repository for software developed for physics-based simulatio...
A trajectory of ribosomal translocation w Internal Coordinate Flexible Fitting ribosome-icf This contains the manuscript, fitted structures, trajectory, and movies for the flexible fitting of ...
Weighted histogram analysis method with Bayesian bootstrapping wham_bb_twod The free energy (or the potential of mean force) along a set of reaction coordinates is a central qu...
ME/BIOE 485 (Modeling and Simulation of Human Movement) me485 This project is a central repository for reading materials, assignments, and student-written compute...
Analysis of arm swing during human walking arm_swing This project provides a simplified version of the UpperLowerBodySimple model from the ULB-project, w...
Comparison of Hexahedral and Tetrahedral Elements in FE modeling of Foot meshcomparison This project compares the performance of hexahedral and tetrahedral elements in finite element model...
Molecular Dynamics Language (MDL) mdl The Molecular Dynamics Language (MDL) is intended to allow users to represent molecular dynamics (MD...
MSMBuilder msmbuilder MSMBuilder is an open source software package for automating the construction and analysis of Markov...
Single Molecule Dwell-time Distributions dwell Dwell-time distributions, waiting-time distributions, or distributions of pause durations are widely...
ADPt-Gromacs - Coupling homologous replicas by adaptive position restraints adpt-gromacs We develop an implementation of adaptive position restraints for the GROMACS MD simulation software....
Upper Extremity Kinematic Model up-ext-model The project holds all the files necessary for a SIMM-based kinematic musculoskeletal model of the hu...
Connecting features of drugs to molecular, cellular, and organismal phenotypes ghf-phd This project contains datasets that I generated for my PhD thesis titled "Connecting chemical featur...
Hydroxyproline Parameters hydroxyproline hydroxyproline parameters for Amber
Ribosomal translocation with EF-G efgtranslocat This project aims at providing new insight about RNA translation into protein, focusing on the trans...