Dear gromacs users,
I am working on a coarse-grained simulation of a model membrane and a synthetic peptide simulation using martini forcefield. At the end of the production run, I am trying to calculate the mass density of the phosphate head groups. I am using the following command: gmx density -f md.xtc -s md.tpr -d z -n head.ndx -symm, now when gromacs is asking for the group around which density is to be centered, I am selecting the SYSTEM and for calculation of density I am selecting PO4 group. However, if I select all the lipids in place of SYSTEM for the density centering, then the values are getting largely modified. What is the correct way to calculate partial densities of different head groups for bilayer simulations in gromacs? Any help would be much appreciated.