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

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 a écrit : > Hi, > Have you tried the following? It usually w

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

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 ha scritto: > Dear Gromacs users, > > I have a d

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

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