[gmx-users] RDF for molecules above a surface

Jingjie Yeo (IHPC) yeojj at ihpc.a-star.edu.sg
Fri Jul 3 08:48:12 CEST 2015

Dear all,

I would like to find out the distribution of molecules above a flat surface, such as the surface of a membrane. Would it be appropriate to be using:
gmx rdf -f run.xtc -s run.tpr -n index.ndx -surf mol -rdf mol_com -pbc

After staring at the manual for really long, I can't quite figure out what exactly is the quantity that will be output. Is it correct to say that this is some kind of non-normalized distribution of the centre of mass of my chosen set of molecules from the surface of the membrane?

Best Regards,

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