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

[Nawel Mele]

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)