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Hello, I have a protein dimer, with each monomer consisting of five chains. I want to use an AMBER force field for the simulation. Do I need to merge all the chains while generating the topol.top file?
Hi, it’s gonna depend on your protein’s underlying structure. If I’m understanding you correctly you have a dimer of pentamers. If that’s true, you wouldn’t merge anything, feel free to leave each ITP separate, and it will all be included in the topol upon creation. If you have a different structure and those pentamers are not physical (i.e. it’s actually a dimer of dimers or something) you’d want to ensure the underlying structure is correct. GROMACS will be easily able to handle any configuration of these things, and pdb2gmx is very robust against high numbers of chains, so just ensure your system is physical.
I performed the simulation without merging the chains; however, the RMSD fluctuations were highly irregular and spiky.