[gmx-users] Using g_densmap

soumadwip ghosh soumadwipghosh at gmail.com
Fri Dec 12 11:59:12 CET 2014

Dear all,
             I am studying the effect of different ion binding to the sites
of a double stranded DNA . I am using GROMACS 4.5.6 and CHARMM force field
for my MD simulations. I have three different simulation results with
sodium, TMA and Choline ions. what I want to do is to make number density
maps using g_densmap in order to show that the preferential occupancy of
these three ions in the regions of the DNA are different, at least in
number. I have made the major and the minor grooves of the DNA in my
index.ndx file in addition to the usual DNA, ions, and SOL groups. I want
to calculate the no. density maps for the ions in the minor groove. So, I
am thinking of writing the command-

g_densmap -f traj.xtc -s topol.tpr -n index.ndx -dt 1000 -amax 6 -rmax 6
-dt 1000 -mirror

Now my question is  from the .ndx file, which are three groups I am
supposed to choose if I want to plot the density map of ions surrounding
the minor groove?

It is written that three groups should be supplied, the centers of mass of
the first two
groups define the axis, the third defines the analysis group.I am a bit
confused which groups should I use as gp # 1, 2 and 3?

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology, Bombay

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