I need to remove PBC effect from a system containing a protein having four monomers, DNA, and metal atoms. I use four commands to remove the PBC effect and it seems to give me the best output possible, but still, I can see slight jumps in the trajectory. I also am concerned about the effect of a bad PBC removal on the resulting structure and its effect on further analysis.
I use -pbc whole, -pbc nojump, -pbc cluster + center, and finally -pbc mol + center.
Any help or comment would be appreciated.
This topic has been addressed several times in the forum. Maybe you find the answer already in the forum using the option search.
Maybe the answer to this post can help
If you want to calculate RMSD respect the starting structure, I suggest to use the option -s with the tpr file of your first step of your simulation (probably EM).