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

jalem...@vt.edu | (540) 231-3129


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