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  1. Chromatophore_Large_System_Simulation Chromatophore_Large_System_Simulation Public

    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…

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  2. ReMDFF_Singharoy_Group ReMDFF_Singharoy_Group Public

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

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  3. NAMD NAMD Public

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

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  4. NAMD_Submission_Scripts_Singharoy_Group NAMD_Submission_Scripts_Singharoy_Group Public

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

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  5. Simple_MDFF Simple_MDFF Public

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

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  6. General_NAMD_Equilibration General_NAMD_Equilibration Public

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

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