GROMACS version: 2020GPU
GROMACS modification: Yes/No
Force filed: Martini 3.0
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I used modeller homology modeling tool to combine three proteins with known structures into a multi-domain recombinant protein structure. This structure and Alphafold3 prediction structure were used for simple protein molecular dynamics simulation.
The recombinant protein has four domains, assumed to be a, b, c, and d.
However, the results obtained from two different initial structures show that the distance between the two domains(a domain and d domain) we are concerned with is too wide.
How do I choose to restructure?