GROMACS version: 2020.3
GROMACS modification: No
Set up will be either: ff14sb/bsc1 + tip3p or ff19sb/bsc1 + ops
The protein complex I want to simulate is long and made of stacked repeating protein chains- too long for us to simulate considering the eventual box size/computational expense. Therefore it will be cropped and lightly restrained at both ends of the full complex during the simulation. Due to the way the protein chains are arranged, some of the individual protein chains will still be their full length and some will not after cropping. So the N and C termini of the cropped chains will not be the real termini in nature. Would it be correct to let the real N/C termini of the full length chains be ionised and the fake N/C termini neutral, since this would be correct normally if the system wasn’t artificially cropped? The restraining of both ends of the complex is for stability and to try and account for the fact the chains would usually continue on and mimic a continuous chain- so the cropped chains will be restrained anyway.