For protein-protein aggregation or protein self-interaction simulations, can gromacs detect the residues that come into contact with each other over the trajectory?
For example, over the trajectory, the proteins can ‘bump’ into each other or be in close proximity at multiple instances, and maybe by listing the most common interacting residues, one can label them as self-aggregation hotspots. Not sure if gromacs has such a function?
It’s worth looking through http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-name to see what analysis GROMACS can perform.
For what you are looking to perform then http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html or http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pairdist.html might be what you are after.
Thanks for the links! Those are quite a lot of methods of analysis. Ill go through each one and try to pick the most suitable one for my work.