[gmx-users] gmx rdf selrpos seltype

[Giuseppe R Del Sorbo]

Dear gmx users,

I am calculating a spherical radial distribution function between the 
center of mass of the methyl group of STS (my surfactant) around the 
center of mass of the STS micelle.

I am using this command:

gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr 
-selrpos whole_mol_com -seltype atom -b 80000  -ref ST -sel C2 -o 
output.xvg

and I get my graph.

If I switch selrpose with seltype and I type:

gmx rdf -f production_NpT.xtc -n index.ndx -s production_NpT.tpr 
-seltype whole_mol_com -selrpose atom -b 80000 -ref C2 -sel ST -o 
output.xvg

I get a different result.


If I well understood, in the first case the reference position is the 
center of mass the micelle

and in the second case the reference position is the methyl group.

Teorically I should get the same result, maybe there is something in 
selrpos and seltype which I missed.

Can anyone help me?

Thanks a lot

Giuseppe