shahrbanoo karbalaee wrote:
Dear justin
thank you.I read pbc subject.and I know that it solve trjconv .now
if I use trjconv after premd . is it still right.?
There is no need. Come to terms with the fact that there is no "inside" or
"outside" of a periodic box, no "left" or "right." There is no need to
manipulate your structures with trjconv between simulations. Just allow
periodicity to do its job. For rendering purposes, yes, use trjconv to align
your solute how you like, but for simulation purposes, don't bother.
-Justin
best
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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