[gmx-users] Removing periodic boundary conditions on a dimer

[Simone Orioli]

Hi,
Have you tried the following? It usually worked for me, but I used to run
simulations on old versions of Gromacs so it might be deprecated.
trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc mol


Il mar 23 apr 2019, 10:51 Nawel Mele <nawel.mele at gmail.com> ha scritto:

> Dear Gromacs users,
>
> I have a dimer system with a ligand in one of the monomer. I am trying to
> remove the periodic boundary conditions to visualise my simulation but
> whatever steps I used the monomers don't want to be centered in the box.
> I tried these steps using a custom index file corresponding to the residues
> near the active site so I would center around them:
>
> trjconv -f system.xtc -s system.tpr -o system_nojump.xtc -pbc nojump
> trjconv -f system_nojump.xtc  -s system.tpr -o system_center.xtc  -center
> -pbc whole -ur compact -n index_file_center.ndx
>
> I am confused on the steps I should be using with these kind of system, do
> you have any suggestions ?
>
> Many thanks,
>
> Regards
>
> --
>
> Dr Nawel Mele,
> T: +33 (0) 634443794 (Fr)
>
> +44 (0) 7704331840 (UK)
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