GROMACS version: 2018.4
GROMACS modification: Yes (modified the oplsaa file)
I built a simulation box containing polymer and four cations. If I have different polymers, let’s say A, B and C. These polymers are of the same type but with modifications. I prepare a different box of varying dimension but with the same distance between periodic images through the gmx editconf -f polymer_A.pdb -o polymer_B.gro -d 1.0. For a particular cation (let say Na), i observed that the position of the 1st and 2nd peaks are same for all polymers. Note that each simulation box contains different number of cation molecules (due to varying dimension) and only one polymer type (either A or B or C). will it be right to compare the intensity of their peaks?