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SIRAH LLPS of FUS-LC #64
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Dear SIRAH Developers,
I recently attempted to use SIRAH-ff to investigate whether it could simulate the phase separation of intrinsically disordered proteins (IDPs), specifically the well-studied FUS-LC. I was motivated by the availability of explicit solvent modeling and the ability to run simulations on a GPU.
For this experiment, I referred to your comprehensive tutorial at https://sirahff.github.io/documentation/Tutorials%20gromacs.html#proteins-in-explicit-solvent, with a few modifications:
Despite these measures, I observed no phase separation. I even employed an annealing scheme in the md.mdp to test various temperatures, extending to non-realistic levels above 400K, to determine if the issue was related to energy scale. Interestingly, the protein condensate became more compact as the temperature increased, which is atypical.
I have attached the *.gro snapshots (the filenames include the time in picoseconds) and the run-mdp file for your review.
Could you please provide any suggestions on optimizing the configuration for liquid-liquid phase separation of IDPs? If further details are needed, I am happy to provide them.
Sincerely,
Gosha
sirah_fus-lc.tar.gz
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