[gmx-users] question about the output of minimization

[Justin A. Lemkul]

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

========================================