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Hello Gromacs users,
I have searched for solutions to atoms across pbc for a while, but none of them actually helps in the situation of self assembly of amphiphiles in aqueous solutions. During simulation, tri-peptides form multiple clusters that may or may not merge into larger ones. Some of these clusters cross periodic boundaries. In order to get unwrapped version of coordinates, I have tried multiple triedgmx triconv commands but none seem to work. -pbc whole option puts the broke molecules together but not broke clusters. -pbc mol or center option just moves clusters in certain directions. -pbc nojump needs a reference frame, and not applicable for a clustering process. The most relevant option seems to be -pbc cluster. It works for the last hundreds of frames where cluster numbers are fewer and cluster sizes are larger, but not the beginning stages(The output trajectory does not match with input at all). I wonder what should be proper unwrapping for the whole self-assembly process.
If post processing is not good enough, would it be a good idea to modify Gromacs source files to directly dump unwrapped coordinates? If so, would anyone kindly point out which file to look at?