Omitting PBC

User discussions
1

Dear all,

Is there any way to omit PBC for simulation run?

I mean fisrtly I can use all steps and equilibrations and then for the final run (md.mdp) I can omit the PBC effect.

Thanks in advance.

2

Hi,
I am not sure I understand your question.
But if the question was,can one run a simulation without periodic boundary condition? Yes, one can run without periodic boundary condition tuning the pbc option in mdp file.
If the issue is how to deal with PBC effect, you can have a look to the following workflow
https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow
Best regards
Alessandra

3

Dear Alessandra,
Thanks for your response.

Yes, I want to run a simulation without PBC. Could you please tell me which line(s) in mdp should be changed?

Best

4

Hi,
in the current version (2021) the option is not active. I think it was still active in 2019 or older version, you have to check the release note (Release notes — GROMACS 2021.2 documentation)
In alternative you can use a very large box. On this topic please have a look at previous posts on vacuum simulation in this forum.
best regards
Alessandra