[gmx-users] question about the output of minimization

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
ah okey. Thank you.
And I have another question. Why is the protein in the corner of the box
and not in the middle?
I thought I centered it with the command:

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

Or not?

>
>
> 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
>
> --
> ========================================
>
> 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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