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

[Nawel Mele]

HI,

I actually just did it after posting this post and the two monomers
appeared to be good (no separated) but the ligand is on the opposite site
and when I tried to center nothing happen.



Le mar. 23 avr. 2019 à 10:54, Simone Orioli <simone.orioli at unitn.it> a
écrit :

> 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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-- 

Dr Nawel Mele,
T: +33 (0) 634443794 (Fr)

+44 (0) 7704331840 (UK)