[gmx-users] Removing periodic boundary conditions on a dimer
simone.orioli at unitn.it
Tue Apr 23 10:54:15 CEST 2019
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,
> Dr Nawel Mele,
> T: +33 (0) 634443794 (Fr)
> +44 (0) 7704331840 (UK)
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users