Preventing Gromacs from wrapping the trajectory

User discussions
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1

GROMACS version: 2020
GROMACS modification: No
Dear all,
It seems that Gromacs by default wraps the output trajectory and keeps the solutes in the simulation box. This approach results in several issues for visualization and analysis that requires post-processing, that in case of complex systems becomes time consuming.
The question is: how can one prevent Gromacs from wrapping the output trajectory and let it write the unwrapped version? Any mdp parameters can achieve this?
Thanks,
Zhaleh

2

There is no mechanism to do this in mdrun. You have to re-image with trjconv later.

3

Thanks Justin for your response. As far as I know NAMD allows one to switch off the wrapping. Could this be a direction that Gromacs may take in the future too?

Thanks,
Zhaleh

4

This gets asked a lot (and actually was just asked a few days ago). There is no functional reason to do this. The calculations don’t depend on a convenient visualization so there’s really no reason to have mdrun spend any time wrapping and reconstructing molecules.

5

Sorry for missing the previous discussions, despite looking around the forum. I understand the rationale. Thanks for the reply.