[gmx-users] question about the output of minimization

[Justin A. Lemkul]

On 7/11/12 7:34 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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.
>

The last line of the .gro file are the box vectors, not the center of the 
system, so you are not, in fact, centering the protein.  You are placing it in 
the corner of the box yourself.  The -center option overrides the -c option.  If 
you want the protein centered, omit -center in your editconf command.

-Justin

> 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
>>>>
>>>> ========================================
>>>>
>>>>
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Only plain text messages are allowed!
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>

-- 
========================================

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

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