[gmx-users] Fwd: Last step before CG em.mdp

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 30 22:47:07 CET 2009

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 

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list