jalemkul at vt.edu
Wed Feb 14 14:11:33 CET 2018
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
jalemkul at vt.edu | (540) 231-3129
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