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amd_namd_simulation

anm_pathway_finder

This repository contains FORTRAN programs to define a minimum energy pathway between to conformational states.

atpase_stalk_analysis

chromatophore_large_system_simulation

Contain herein are scripts for making an all atom model of a chromatophore from Rhodobacter sphaeroides, as well as configuration scripts for MD and BD simulations of the aforementioned model using the simulation package NAMD. Additionally, there are scripts to run APBS calculations.

general_namd_equilibration

These scripts are meant to build, minimize and equilibrate as system

mdff_error_analysis

Herein are scripts for analyzing the error term in the MDFF grid potential.

mdff_map_n_model_maker

mdff_multimap_smd

mdff_workshop

This repository is meant for ASU's Coding Boot camp Workshop. Herein are files necessary for running a MDFF simulation.

namd

This repository contains NAMD input generation, simulation, and analysis scripts.

namd_equilibration

namd_submission_scripts_singharoy_group

Included in this repository are NAMD job submission scripts for both LSF and Slurm job management systems.

remdff_singharoy_group

This repository contains scripts for running Resolution Exchange Molecular Dynamics Flexible Fitting using the NAMD macromolecular simulation engine.

simple_mdff

This repository contains scripts for running simple Molecular Dynamics Flexible Fitting simulations with the NAMD engine.