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

[Justin A. Lemkul]

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

-- 
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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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