Atoms renumbering

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No
Hi all,

I wrote a section of a .gro file with trjconv using an index, but the atoms are renumbered in the new .gro file:
Original .gro:

(...)
104TIP3   OH2  310   2.533   2.588   2.179  0.1968 -0.5520 -0.2968
104TIP3    H1  311   2.581   2.511   2.150  1.3339 -0.2456  0.6895
104TIP3    H2  312   2.495   2.563   2.263 -1.1699 -0.6914 -0.9294
(...)
128TIP3   OH2  382   2.246   3.223   2.960 -0.0413 -0.2121 -0.7616
128TIP3    H1  383   2.310   3.267   3.016 -0.2133  0.7772 -1.3384
128TIP3    H2  384   2.184   3.291   2.935 -0.2262 -0.7393 -1.7984
(...)

New .gro file:

(...)
  104TIP3   OH2    1   2.533   2.588   2.179  0.1968 -0.5520 -0.2968
  104TIP3    H1    2   2.581   2.511   2.150  1.3339 -0.2456  0.6895
  104TIP3    H2    3   2.495   2.563   2.263 -1.1699 -0.6914 -0.9294
  128TIP3   OH2    4   2.246   3.223   2.960 -0.0413 -0.2121 -0.7616
  128TIP3    H1    5   2.310   3.267   3.016 -0.2133  0.7772 -1.3384
  128TIP3    H2    6   2.184   3.291   2.935 -0.2262 -0.7393 -1.7984
(...)

How can I avoid this renumbering to keep the original atom numbers?

Thanks in advance.

Best.

2

Pretty sure the code does it by default, unfortunately. Have seen mentioned that are plans to rework various parts of the code to not do things like this.

As a solution to your current problem, you might have to write your own code to return the atom numbers back to how you want them to be.