[gmx-users] how to optimize the orientation of the protein in a dodecahedron

Thu Apr 26 16:09:19 CEST 2012

Hi Thomas,

Apologies, you are right. I was thinking of the distance to the wall.
If the protein is elongated, it will matter in the minimal distance
whether the protein major radius is oriented towards a face or towards
a corner. In addition, the shape of the protein plays a role. Yet it
doesn't really matter for the setup of the simulation, since the
rhombic dodecahedroon is built according to the radius of the system,
added the distance to the wall (-d). The rhombic dodecahedron is
constructed based on the inscribed sphere with that radius, such that
every orientation will satisfy the minimal distance between images.
For a given solute, the rhombic dodecahedron is uniquely defined,
regardless the orientation, in contrast to what happens with a
rectangular unit cell.

I hope this clarifies things.

Cheers,

Tsjerk

On Thu, Apr 26, 2012 at 3:57 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
> Hi Tsjerk and Erik,
>
> Thanks for the comments. It's strange, because I get different minimum
> distance for different orientations of the same protein structure using the
> afore-mentioned command lines. I used a single step energy minimization for
> speed (em_real.mdp). Below are the outputs of editconf and the last lines of
> the output .gro files. There are differences in the Volume (884.007 nm^3
> versus 996.803 nm^3), system size, center, box vectors, box volume, and
> shift. What do these differences mean? Can they explain the different
> mindist I get?
>
> ##
> ## Protein Orientation 1 editconf_4.5.5 output:
> ##
>
> Read 17463 atoms
> Volume: 884.007 nm^3, corresponds to roughly 397800 electrons
> No velocities found
>     system size :  9.205  8.440 11.378 (nm)
>     diameter    : 12.498               (nm)
>     center      :  6.524  6.242  9.385 (nm)
>     box vectors :  9.205  8.440 11.378 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  : 884.01               (nm^3)
>     shift       :  3.226  3.508 -4.789 (nm)
> new center      :  9.750  9.750  4.596 (nm)
> new box vectors : 13.000 13.000 13.000 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  :1553.51               (nm^3)
>
>
> ## Last line of the output .gro file:
>   13.00000  13.00000   9.19239   0.00000   0.00000   0.00000   0.00000
> 6.50000   6.50000
>
> ## g_mindist output:
>
> Last frame          0 time    2.000
>
> The shortest periodic distance is 1.5735 (nm) at time 2 (ps),
> between atoms 992 and 8506
>
>
> ##
> ## Protein Orientation 2 editconf_4.5.5 output:
> ##
>
> Read 17463 atoms
> Volume: 996.803 nm^3, corresponds to roughly 448500 electrons
> No velocities found
>     system size : 12.299  9.828  8.247 (nm)
>     diameter    : 12.498               (nm)
>     center      :  5.898  4.759  8.713 (nm)
>     box vectors : 12.299  9.828  8.247 (nm)
>     box angles  :  90.00  90.00  90.00 (degrees)
>     box volume  : 996.80               (nm^3)
>     shift       :  3.852  4.991 -4.117 (nm)
> new center      :  9.750  9.750  4.596 (nm)
> new box vectors : 13.000 13.000 13.000 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  :1553.51               (nm^3)
>
> ## Last line of the output .gro file:
>   13.00000  13.00000   9.19239   0.00000   0.00000   0.00000   0.00000
> 6.50000   6.50000
>
> ## g_mindist output:
>
> Last frame          0 time    2.000
>
> The shortest periodic distance is 2.59235 (nm) at time 2 (ps),
> between atoms 3915 and 6814
>
>
>
> Thanks in advance,
> Thomas
>
>
>
> On 26 April 2012 15:36, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hey Thomas,
>>
>> The rhombic dodecahedron corresponds to the packing of a sphere.
>> Consequently, the difference in the distance between periodic images
>> over the shortest diameter and the longest diameter is pretty small.
>> That means that there isn't really an optimal orientation in a rhombic
>> dodecahedron; all orientations are pretty much equal. And that's how
>> it should be :)
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis <tevang3 at gmail.com>
>> wrote:
>> > Dear GROMACS users,
>> >
>> > I have noticed that for constant box dimensions the minimum distance
>> > from
>> > the periodic images of a protein depends on the initial orientation of
>> > the
>> > protein, whereas the orientation of the dodecahedron relative to the
>> > x,y,z
>> > axes remains fixed. These are the command lines I use:
>> >
>> > pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff
>> > amber99sb-ildn -water tip3p -ignh
>> > # set the new dodecahedron box dimensions
>> > editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o
>> > protein_box.gro
>> > # solvate with TIP3P
>> > genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro
>> > -p
>> > protein.top
>> > # add ions
>> > grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o
>> > protein_ions.tpr
>> > echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p
>> > protein.top
>> > -pname NA -nname CL -np 3
>> >
>> > grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o
>> > protein_EM.tpr
>> > mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM
>> >
>> > # to see a dodecahedron
>> > echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s
>> > protein_EM.tpr -o em_dodecahedron.xtc
>> > # measure the minimum distance from the periodic images
>> > echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi
>> >
>> >
>> > Is there any way to optimize the orientation of protein inside the
>> > dodecahedron in order to get the maximum possible mindist?
>> >
>> >
>> > Thanks in advance,
>> > Thomas
>> >
>>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands