GROMACS version: 2023.2
I am using Gromacs to conduct MD simulation. The protein chain I am utilizing contains two chains. And it is necessary to retain both chains, as they both contain crucial conformational sites. When I use both chains, however, I obtain very unconventional results, whereas when I use a single chain, I obtain conventional results. I have reviewed every file and methods. But was unable to solve it. For protein topolgy, I used the charmm36 force field. And CGenFF server was used to generate ligand topology. Can anyone please help to solve the error ?
First Figure - Both protein Chains
Second Figure - Only one protein Chain.
