[gmx-users] g_sdf

[Nilesh Dhumal]

Hello,

I have a system with glucose + ionic liquids (cation + anion).

I am trying calculate distribution of cation and anion around glucose
molecule using g_sdf. I want to plot distribution of cation and anion is
same figure. I run the following command

g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128-no.ndx -mode 2 -o -r

I selected two atoms from glucose and 3rd and 4th groups are cation and
anion respectively.

All the coordinates in  refmol.gro are zero.

I am using gromacs version 4.0.7.

Why all the coordinates in  refmol.gro are zero.

Thanks

Nilesh