[gmx-users] g_sdf

Justin A. Lemkul jalemkul at vt.edu
Sat May 21 18:33:31 CEST 2011

Nilesh Dhumal wrote:
> 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.

g_sdf is relatively inflexible; it was designed (it appears) around calculations 
involving water.  g_spatial is much more flexible, and I believe it was for this 
reason that g_sdf has been removed from newer Gromacs versions.  Try g_spatial 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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