GROMACS version: 2022.4
GROMACS modification: No
Hello :)
I’m newbie in Gromacs, struggling with MD simulation.
I need to process MD simulation with 2 proteins in comfined space,
to analyze protein-protein interaction,
so I tried some ways.
but it seems gromacs basically supports pbc,
so eventhough I make MD box size very small,
two proteins are not always stick together, and seperated.
(I tried 1 ms MD simulation, but after 260 ns, two protein seperated and never attached again until end of simulation)
Is there any way to solve this situation?
How can I comfine the MD simulation space, so peptides are not seperated that much?
Thanks for everyone,
happy new year :)