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Hello,
I am investigating dimer formation of a membrane protein using a coarse-grained GoMARTINI model in a neuronal membrane system.
System setup
· CG monomer structure: protein_cg.gro
· Second monomer generated using:
gmx insert-molecules -f protein_cg.gro -ci protein_cg.gro -nmol 1 -radius 4.5 -o two_monomers.gro
· The two-monomer system was then embedded into the membrane (attached images).
· Energy minimization, followed by NVT and NPT equilibration, was performed.
· After embedding and minimization, the COM distance between monomers was ~9 Å.
Issue
After membrane embedding:
· One monomer appears properly embedded and aligned with the membrane normal.
· The second monomer is slightly tilted/rotated relative to the first.
· I am only able to translate or rotate both monomers together, not individually.
· Even after equilibration, there was no significant change in the relative orientation.
I am unsure whether:
· This slight rotational deviation is expected during membrane embedding,
· Or if it indicates improper insertion or orientation prior to embedding.
Questions
1. Does gmx insert-molecules introduce random rotational orientations for inserted molecules?
2. If so, what is the recommended workflow to ensure two monomers have identical orientation before membrane embedding?
3. Is ~9 Å COM separation too close for an unbiased dimerization study in MARTINI CG simulations?
4. If the system remains stable during equilibration, can this orientation difference be considered acceptable?
I would be grateful for any advice or recommendations regarding best practices for preparing a controlled dimer setup in membrane coarse-grained simulations.
Thank you
