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.
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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