I have a question about the output of the “gmx density”.
If we include the options “-d X/Y/Z”, the output is the distribution of the density along that axis, respectively. It means the horizontal axis, named “coordinate” in the .xvg file, is the axis X/Y or Z.
If we don’t include, the coordinate is automatically the radius, isn’t it?
And, for our project, we need to determine the density distribution of our protein, along its symmetrical axis. Is there anyway to do it?
Thanks a lot, in advance!
I’d greatly appreciate your guidance.
So, is the Z-axis automatically in use when the option is not specified, i.e. when the “-d X/Y/Z” is not included in the command?
And, are the slices along the X and the Y axes are automatically picked to be the same values?
I made that guess based on our output, but not 100% sure.
For example, we run these four commands on the same target trajectory, to compute the density of Water group (TIP3P216 model), based on the center of the Protein Group.
(1) gmx density -f full.xtc -n index.ndx -s full.tpr -o density_water_?.xvg -center
(2) gmx density -f full.xtc -n index.ndx -s full.tpr -o density_water_X.xvg -center -d X
(3) gmx density -f full.xtc -n index.ndx -s full.tpr -o density_water_Y.xvg -center -d Y
(4) gmx density -f full.xtc -n index.ndx -s full.tpr -o density_water_Z.xvg -center -d Z
And here are the output respectively,
(First column is “Position in nm”, and the second is “Density in kgm^(-3)”.)
(1) Not including -d
“…
-0.718345 903.513
-0.513104 896.691
-0.307862 894.742
-0.102621 895.902
0.102621 899.714
0.307862 906.809
0.513104 916.62
0.718345 926.764
…”