[gmx-users] pbc

Justin A. Lemkul jalemkul at vt.edu
Fri Dec 12 12:54:47 CET 2008

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.


> best


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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