Finding the coordinates of atoms from .xtc file

User discussions
1

GROMACS version:2020
GROMACS modification: Yes/No
After MD Simulation of collagen how can i find the atomic coordinates of the following from .xtc file
(“GLY, CA-atom from chain A”)
(“PRO, CA-atom from chain B”)
(“HYP, CA-atom from chain C”)

2

I like to use MDTraj for that purpose - once you load your simulation, you can do:

t = md.load(...)
selection = t.top.select('resname GLY and name CA and chained 0')
coords = t.xyz[:, selection, :] # all frames, selected atoms, all 3 coordinates

…and then continue with a simple 3D NumPy array.

1 Like
3

(Sorry, should be “chainid”, I just noticed the typo now)

4

As @milosz.wieczor said, there are several tools, like MDTraj or MDAnalysis if you are familiar with python, that let you play around.

Personally, if I just need something fast I use gmx traj, which will give you positions as a function of time, among other things. However, you will need the .tpr file as well.