[gmx-users] steady

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 9 14:44:15 CEST 2008

shahrbanoo karbalaee wrote:
> Dear justin
>  a) if  I want  to have the steady and hemogen for mix solvent  , do I
> have to use this command (when I made genbox box 16.16.24 before
> that)?
> :editconf  -f conf.gro -bt dodecahedron -d 0.5 -o box.gro

This will not homogenize anything; it only sets up the initial system.  To get a 
homogeneous box you have to equilibrate (sometimes for a very long time).

> b) I use trjconv -pbc mol  -ur compact and then minimize .when I see
> the output this part in vmd or ngmx and around X-rotate.I will see
> water in top and tfe in down box and another roatation the box is
> seemed hemogen ous .is it correct?

No.  Using -pbc mol -ur compact is a post-processing trick to visualize.  If you 
use the trjconv output in a simulation, it's likely to go screwy, since Gromacs 
determines periodicity from a triclinic unit cell.

Create your system (using -bt dodecahedron is fine, but will likely look like a 
rectangle in VMD or ngmx), and minimize.  Use the output of the minimization for 
your equilibration simulations.  If you want to visualize a dodecahedral box, 
then use trjconv, but do not use this altered file for simulations.


> about distortion ,my mean is"donot have periodicity and hemogenity"
> thanks and appreiciate u


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


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