Justin A. Lemkul wrote:
Then that's certainly the first problem to fix. This is why I generally
use editconf for defining the box (and why I keep recommending it). For
a simple protein in water, using a command like:
editconf -c -d 1.0
will define a suitably-sized box so that you don't have to guess at the
box dimensions. There is no such option with genbox.
And it must be the start to a long week, as I'm already getting forgetful. The
above command will define a rectangular box, which, in general may not be
applicable for, i.e., a globular protein in water (due to the likelihood of
rotation during diffusion). In such a case, you're better of with a rhombic
dodecahedron:
editconf -c -d 1.0 -bt dodecahedron
For a membrane system, you will likely need a cubic or rectangular box, due to
the inherent shape of the bilayer. But for the sake of thoroughness of the
archive, I thought I'd mention that.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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