How to fix my simulation in the center of the box?

User discussions
1

GROMACS version:2020.4
I would like to ask about the possibility to fix my structure in the center of the box during the simulation as the structure get distortion when the structure moves to the edge of the box and I would like to ask if my extra ted data will be affected when the distortion happened on the edge of the box

2

Hi,
if you run a simulation using periodic boundary condition, you do get any distortion at the edge of the box. Your trajectory may look strange, but it is mainly a visualization problem. You can use trjconv to post process your data (you find several posts on this topic in the forum) .
Best regards
Alessandra

3

Thanks for helping … done

4

@alevilla
I wonder if it’s possible to write and include in the manual a more practical gmx_trjconv guide.
Looking at repetitious questions about PBC removal both on the old mailing list and on this forum, it looks like it’s a pretty ubiquitous problem and probably presents a major hurdle and a rather frustrating exercise for inexperienced users.

5

Good suggestion. There was an old documentation page on this, but it will be good to have a new one.
Anyway here I post the old page
http://www.gromacs.org/Documentation_of_outdated_versions/Terminology/Periodic_Boundary_Conditions

Alessandra

6

From my experience, 99% of issues are handled by gmx trjconv -pbc mol -center and choosing a suitable solute molecule for centering. The issues that get reported are usually for corner cases for which imaging is going to be hard for just about any software (except for autoimage in cpptraj, which is apparently magic, but also makes some assumptions :)

1 Like
7

@alevilla note that the current manual has this and could be updated if someone was so inclined.

https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow

The longstanding problem is that trjconv tries to do too much in one program, so it requires complex usage for complex systems.

8

@jalemkul
Thank you, Justin! I had in my brower the old page, but the content is very simular.
I still think that more examples may be useful in the documentation, before new post-processing tools may/will be released (probably a final and more elegant solution).
Best regards
Alessandra

9

Yeah, compare it with pages of “Installation guide” or Getting good performance from mdrun". They both are much more detailed and illustrated, even have some functional examples.
Not to mention that this PBC page is hard to locate in the first place.

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What would you suggest for an improvement?