Contained 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.
Below are links to the chromatophore structure file, gridpdb file and map file required to run the NAMD simulation. https://drive.google.com/a/asu.edu/file/d/10gVADYl320HJiNoe4ilagAKoI7UeR638/view?usp=sharing https://drive.google.com/a/asu.edu/file/d/1MZpm3ABXIPjfbKYLOZOSKbmQJZx4yma1/view?usp=sharing https://drive.google.com/a/asu.edu/file/d/1v9Ni3OlrG45qfA5bO2meIc5xwxT8A1En/view?usp=sharing
Below here is a link to the Movies of the submitted manuscript. https://drive.google.com/a/asu.edu/file/d/1N4GmSsWBGxJVrYXVWBHhP-Stf5ASWkZx/view?usp=sharing