[gmx-users] interpretation of g_potential

soumadwip ghosh soumadwipghosh at gmail.com
Mon Sep 15 15:04:18 CEST 2014

Dear GMX users,
                      I want to calculate net charge distribution from a
simulation of DNA in presence of MgCl2. I did the following-

My command line looks like -
 g_potential -f nopbc.xtc -s md.tpr -p topol.top -n index.ndx -o

Now I obtained three files -
1. potential.xvg
2. charge.xvg
3. field.xvg.

I selected Mg2+ and DNA group when prompted.I am interested in the  .xvg
file since it contains the charge density values against slabs of the box
length. Now, in this file, most of the values are negative. Why is it like
this? Am I doing something wrong?

The reason why I need this is I want to have a plot of r vs charge density
and from there I wish to multiply it by 4*pi* r^2 and then integrate it in
Origin software to obtain the net charge distribution function.

If I am doing wrong, is there any other way to calculate charge density in
GROMACS or to calculate the net charge distribution in general.

Thanks in advance.


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