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.