GROMACS version: 2021.5
GROMACS modification: No
Hello I’m trying to calculate the radius of the first hydration shell of a 13 amino acid peptide using
*gmx rdf*.
I’ve performed a 1µS simulation of this peptide in a cubic water-box of 6nm each side. Starting with the peptide in the box center.
I was using the following command:
gmx rdf -f md.xtc -s md.tpr -ref Protein -sel SOL -o rdf
I expected two or three discrete peaks, but I got this mess:
I’ve tried 29 combinations of options for the *-selrpos -seltype -norm -excl -cut and -surf* but nothing seems to work. I’ve also tried using trajectories processed with -pbc mol and -pbc whole.
As this research was not yet published, I cannot disclose all of my files yet.
I’m kind of out of ideas, I went through all posts with thegmx rdf in them, and also many pages on google but wasn’t able to find anything helpful. Any help will be really appreciated.
Thank you.