How to determine the cell size range (cubic) for converged protein conformation

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GROMACS version:2022.02.22
GROMACS modification: Yes/No
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Greetings Gromacs users,

I have conducted 4.8us simulation, and I have obtained (single pdb) converged conformation of protein. I extended this replica simulation with mutations for about 1ns (trial) with box size 0.5 and 1nm respectively. My question is that whether, how to determine good box size range, so I can speed up simulation timing. I know gromacs default size is 1nm, this size pack lots of water molecules (>250k) with TIP4P model which will slow down my simulations eventually. I also conducted reduced the box size of simulation, however not sure if the box size is good enough (0.5nm). Do I have to consider the density, total energy and potential energy of production run from 0.5nm box size (trial)? or what type of other parameters I should check to ensure the box size is sufficient enough to avoid any issue with PBC.

Thank you for your time and assistanc

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Hi,
Did you try to use rhombic dodcahdron type of box? See
https://manual.gromacs.org/current/reference-manual/algorithms/periodic-boundary-conditions.html#some-useful-box-types

Best regards
Alessandra

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Thank you for your prompt reply.Yes, I tried rhombic dodecahedron as well as octahedron. I am not sure which one better because octahedron will give my better speed overall by packing less molecules, but trajectory density has higher fluctuations in octahedron compare to cubic.(at least plot of time vs density suggested), however to understand the true difference will conduct some statistical analysis (Anderson-Darling Test). Do you think it would be a good idea to just carry on with octahedron??

Thank you for your assistance and time.