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.
Dear Prasad
In my view, you could visualize the final configuration in MD step by VMD software for example which allows you to detect the number of NA which did not adsorb, and then you could index them and use them for RDF analysis.
Hope it helps
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