[gmx-users] question about the output of minimization

[Justin A. Lemkul]

On 7/11/12 6:13 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I did a minimization of my structure. But the output seems a bit strange
> for me, since my input was the protein with its membrane in a box like
> this:
> # = box  P = Protein  M=Membrane
>
>
> #############
> #      PPPP #
> #     MPPPPM#
> #      PPPP #
> #           #
> #           #
> #############
>
> But the output of the minimization looks like this
>
> #############
> #        PPPP#
>   #M     MPPPP #
>    #      PPPP  #
>     #            #
>      #            #
>       ##############
>
> How can that be?

It's a triclinic representation of the unit cell.  Nothing is wrong.

> My box was created with:
>
> editconf -f wholeProtein.gro -o 3m71_box.gro -center 4.59340   4.59470
> 5.17330 -c -bt dodecahedron -d 1.0 2>>logErr 1>>logOut
>

Is a dodecahedral box appropriate for a protein in a membrane?  The inherent 
symmetry of a slab of any sort dictates that you should be using a cubic or 
rectangular box.  Dodecahedral and octahedral boxes are better for systems with 
spherical symmetry, like globular proteins in water.

>
> I put solvent in it with:
>
> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
> 2>>logErr 1>>logOut
>
>
> The mdp file for the minimization looks like this:
>
> define                  = -DPOSRES
> integrator              = steep
> emtol           = 10
> nsteps          = 1500
> nstenergy               = 1
> energygrps              = System
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw                    = 0.9
> rlist           = 0.9
> fourierspacing  = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> pbc                     = xyz
>
>
> Can you please tell me how I can prevent my box to shift?
>

There is no box shift; it's just a visual representation of the dodecahedral 
box.  You can "correct" it (for visualization purposes) by running trjconv -pbc 
mol -ur compact.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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