Calculate peptide first hydration shell gmx rdf

User discussions
1

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:

rdf
rdf553×612 3.36 KB

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.

2

Try fixing this by conducting the RDF between the oxygen atoms of the water molecules and the backbone atoms on the peptide. You can do this by gmx make_ndx -f md.tpr -o index.ndx, then a OW then q. Then run gmx rdf -f md.xtc -s md.tpr -ref Backbone -sel OW -o rdf.xvg