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

[Tsjerk Wassenaar]

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