Rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

GROMACS version:2020.2
GROMACS modification: No
Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For instance, I was trying to do it as follows

gmx rdf -f …/md_0_1.xtc -s …/md_0_1.tpr -selrpos mol_com -seltype atom -bin 0.05 -nopbc -ref ‘(resname SI NA) and within 0.4 of resname SI’ -sel ‘(name OW)’ -o test.xvg

where SI is the nanoparticle, however it will also cover nanoparticle surface in the rdf calculation and in my case I need only around NA ions that are adsorbed on nanoparticle. Any help would be appreciated, thanks in advance.

you can use as ref group Na+ within a defined distance from the silica (?) surface. Here you can find more on< selection expression>

I hope it helps


Hi Alessandra, thanks for the reply basing on the inputs I have changed the command as followed
gmx rdf -f …/md_0_1.xtc -s …/md_0_1.tpr -selrpos mol_com -seltype atom -bin 0.05 -nopbc -ref ‘resname NA and within 0.4 of resname SI’ -sel ‘name OW’ -o test.xvg
however, I just want to clear that 0.4 (nm) distance is from the surface of SI or from the center of mass of SI? Thanks, in advance.