OpenABC simplifies simulation setup with Python scripting.
The example code includes all the steps necessary for setting up and performing MD simulations of a protein condensate with MOFF and default settings in a cubic box of length 100 nm. The ten lines included in the highlight box correspond to the creation of the condensate system by parsing topological information from an initial PDB file, building a configuration file by inserting molecules into a box and incorporating the molecular objects, protein, into a container class, condensate, with appropriate force fields. The rest of the code includes standard simulation setups generic to OpenMM. We chose the Langevin middle integrator to perform simulations at 300 K with a friction coefficient of 1 ps−1 and a timestep of 10 fs.
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