In gmx mdmat command, how can I place the general axis of my molecule along one of the x, y, or z ax

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Hello

I use the " gmx mdmat " command to analyze the molecular dynamics results of my research. My protein is three alpha helices that are parallel to each other.

gmx mdmat -f md_0_1.xtc -s md_0_1.tpr -mean mdmat.xpm -frames mdmat2.xpm -no mdmat.xvg

In this command, how can I place the general axis of my molecule along one of the x, y, or z axes in the box?

2

mdmat doesn’t depend on orientation. It simply computes a distance matrix, which will be the same no matter how your species are rotated. If you want to reorient anything in your system, use trjconv.

4

Thanks.
I did the “gmx mdmat” command as follows:

gmx mdmat -f *.xtc -s *.tpr -meaning *.xpm -frames *.xpm -no *.xvg

and use “gmx xpm2ps -f *.xpm -di *.m2p -o *.eps” to make contacts map between residues. But in the output diagram, which I attached, the order of the amino acids on the x and y axes is disturbed. How can I fix the error?!

mdmat
mdmat620×625 24.8 KB