GROMACS version: 2021.3
GROMACS modification: Yes/No
Dear all,
I am relatively novice at MD simulations. I have performed a 1-microsecond simulation of a certain protein that my lab is studying inside a solvation box. I have utilized the AMBER ff19SB force field for the protein with TIP3P water. Now, I wish to study the hydration shell around my protein, for which I employed VMD’s RDF tool.
Before this, I corrected my trajectory for PBC effects using a three step trjconv procedure: (i) -pbc whole, (ii) -pbc nojump, (iii) -pbc mol -center with “Protein” selected for centering.
This is the plot I’m getting when plotting between oxygen atoms of water and protein’s backbone.
And, this is when I’m plotting between oxygen of water.
I need your help in deciphering these plots as I have limited knowledge about how to read RDF plots and cannot decide if these are correct. I understand the bare mathematical definition but nothing beyond it. I am happy to take this post down if this doesn’t belong to this forum. Thanks a lot in advance!