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

[Erik Marklund]

Hi,

And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum.

Erik

26 apr 2012 kl. 14.36 skrev 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
> --
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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