Pinned Repositories
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
NAMD
This repository contains NAMD input generation, simulation, and analysis scripts.
ReMDFF_Singharoy_Group
This repository contains scripts for running Resolution Exchange Molecular Dynamics Flexible Fitting using the NAMD macromolecular simulation engine.
jvant's Repositories
jvant/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.
jvant/NAMD
This repository contains NAMD input generation, simulation, and analysis scripts.
jvant/ReMDFF_Singharoy_Group
This repository contains scripts for running Resolution Exchange Molecular Dynamics Flexible Fitting using the NAMD macromolecular simulation engine.
jvant/AMD_NAMD_Simulation
jvant/ANM_Pathway_Finder
This repository contains FORTRAN programs to define a minimum energy pathway between to conformational states.
jvant/ATPase_stalk_analysis
jvant/General_NAMD_Equilibration
These scripts are meant to build, minimize and equilibrate as system
jvant/MDFF_Error_Analysis
Herein are scripts for analyzing the error term in the MDFF grid potential.
jvant/MDFF_map_n_model_Maker
jvant/MDFF_MultiMap_SMD
jvant/MDFF_Workshop
This repository is meant for ASU's Coding Boot camp Workshop. Herein are files necessary for running a MDFF simulation.
jvant/NAMD_Equilibration
jvant/NAMD_Submission_Scripts_Singharoy_Group
Included in this repository are NAMD job submission scripts for both LSF and Slurm job management systems.
jvant/Simple_MDFF
This repository contains scripts for running simple Molecular Dynamics Flexible Fitting simulations with the NAMD engine.