[gmx-users] how to compute the solvent density distribution, around solute and visulize it

Chris Neale chris.neale at utoronto.ca
Tue Dec 9 19:22:19 CET 2008

Without further indications of what your problem is it is not very easy to help you.

You could try g_spatial with the VMD "volume slice" representation.


--- original message ---

    I would like to compute the solvent density distribution around solute and visualize the solvent density maps around solute. I have read the manual and known the g_densmap could do it. I have carried out the g_densmap as follow, 
    g_densmap -f traj.xtc -s topol.tpr -n index.ndx -bin 0.1 -n1 6 -n2 6 -amax 3 -rmax 6 -mirror -unit count -o densmap.xpm
    xpm2gs -f densmap.xpm -nice 10 -size 400 -rainbow -o plot.eps

   But the plot.eps is not the figure in the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0812092310359766_0.jpg 
   I want to know more details about how to get the figure in the link. it is appreciated if you could give me some suggestion

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