[gmx-users] question about the output of minimization

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

Yes I tried the command you wrote but it is still in the corner of the box.
Is there anything else I can do?
The coordinates I used to center the protein are the ones which are in the
last line of the .gro file.

Thank you

>
>
> On 7/11/12 7:12 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> 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?
>>
>
> Have you tried trjconv -pbc mol -ur compact?  The "center" of an infinite
> system
> is an arbitrary location; you have to re-wrap the unit cell to achieve the
> expected outcome.  It's centered, it just may not look like it in the
> current
> representation.
>
> -Justin
>
>>>
>>>
>>> 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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>>
>>
>>
>
> --
> ========================================
>
> 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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