GROMACS version: 2018
Hi, I am trying to calculate the intermolecular distance between centeres of mass of a protein and a ligand molecule. For this purpose I have first corrected my trajectory for pbc related artifacts using:
gmx trjconv -f prod.xtc -s prod.tpr -pbc mol -o nopbc_prod.xtc, selected the entire system for output
then used gmx distance: gmx distance -f nopbc_prod.xtc -s prod.tpr -select ‘cog of group “LIG” plus cog of group “PROT”’ -oav -oall -oxyz;
Now my question is that for intermolecular distance calculation or distance between two different molecules or two groups that are part of two different molecules, it is required to use minimum image convention or one can get away without using that (say setting -nopbc flag in gmx distance) after correcting trajectory from pbc artifacts; If I use -nopbc will I be getting correct distances as gromacs always takes nearest minimum image of a particle in account for distance or interaction calculation; For intramolecular distance calculation or calculating distances between two atoms of the same molecule, I suppose -nopbc flag is probably going to be the right choice, else due to minimum image convention gromacs can give spurious results for intramolecular distances , e.g. end-to-end distance of a protein.