[gmx-users] PBC

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 14:11:33 CET 2018

On 2/12/18 8:44 AM, Ahmed Mashaly wrote:
> 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

You can use whatever reference coordinates you want. Energy minimization 
generally shouldn't result in large structural changes, so make sure you 
have a sufficiently large box to avoid spurious minimum image interactions.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list