[gmx-users] PBC

[Ahmed Mashaly]

Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference (-s) .tpr should be the one I used in simulation (md.tpr) or I can use the first one (em.tpr) without a difference?

This is because the protein has jumped after em step, and if I have to use md.tpr as reference for md.xtc, I will have to recenter it after every step of em, nvt, npt
Kind Regards,Ahmed