[gmx-users] steady

Berk Hess gmx3 at hotmail.com
Thu Oct 9 14:52:39 CEST 2008

> Date: Thu, 9 Oct 2008 08:44:15 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] steady
> 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.
> -Justin

This post processing by trjconv with -pbc and -ur only changes which periodic
copy of a molecule or group is used.
Such configurations can be used for simulations without problems,
since the actual structure did not change.
mdrun will put things back in the periodic cell it wants at startup
(unless the continuation is turned on in Gromacs 4).


> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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