Rdf between Centre of mass of a molecule and a cation

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1

GROMACS version:
GROMACS modification: Yes/No
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I am facing problem during the calculation of rdf between a centre of mass of a molecule and a cation.
I tried the -selrpos -seltype options but using this the rdf I am getting is wrong … there is an extra peak coming… but there is no problem when I am calculating the rdf between the centre of mass of two molecule using selrpos and seltype options. And also there is no problem during the calculation of rdf between two atoms in normal way.
Please help me out why only this problem is arrising during the calculation of rdf of centre of mass of a molecule and a cation or atom.

2

Hi,
can you post the command line that you use? and something more on the system, e.i is the cation composed of one atom or more atoms?
Thank you
Alessandra

3

Command line
gmx rdf -f .xtc -s .tpr -selrpos mol_com -n index.ndx -ref 0 -sel 1 -o rdf.xvg
Cation is monovalent cation like Li, Na etc.

4

your problem fixed?

5

yes
gmx_mpi rdf -f md.xtc -s md.tpr -ref ‘mol_com of group 2’ -sel ‘group 3’ -o rdf.xvg
this is the command