I want to calculate RDF between OW(water) and N+(nitrogen in PPO polyelectrolyte chain) to investigate water hydration layer. The RDF I calculated was very different regard to similar articles. Actually, it must give first high pick in about 4-5 A but my RDF is like a picture I attached here. There are three picks that is a bit strange. what is the main problem?
I used following command:
gmx rdf -f npt.xtc -s npt.tpr -b 90000 -e 120000 -o rdf.xvg -ref"com of group N" -sel" com of group OW" -n index.ndx
in index.ndx I selected N+ and OW atoms
[N]
29 129 …
[ow]
787 656 …
Thank you in advance
What happens if you compute a normal atom-based RDF? The COM RDF is going to be very weird for such a system. Also note that gmx rdf makes no attempt to correct for excluded volume effects (AFAIK), which may be significant in polymeric systems.
Dear Lemkul
Thank you for your constant attention and response. To be honest, I thought this is the only way to compute RDF. What is the difference between normal atom based RDF and COM? how can I use that? is there any specific flags for that?
Dear sir,
GROMACS version:2023.1
GROMACS modification: No
Here post your question
hi,everyone,
i have a micelle composed of 40 molecules A, and i have a drug molecule B. i wang to caculate the rdf function between the center of mass (com) of the micelle and drug B, but i can not get a proper result.( the drug was on the surface of the miclle ,but the rdf was not right.
my rdf is caculated by :
gmx rdf -f trajout.xtc -s md.tpr -ref “com of group A” -sel “com of group B” -pbc -bin 0.1
Please put (-b) and (-e) in your command in the first try to fix the problem. Note that, consider the last part of your production run ( e.g., -b 85000 ps to 95000 ps for 100 ns of run). Also, it is better to define the .ndx file in which you specified indexes of desired groups.
