<div class="gmail_extra">Hi Tsjerk and Erik,<br><br>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?<br>
<br>##<br>## Protein Orientation 1 editconf_4.5.5 output:<br>##<br><br>Read 17463 atoms<br>Volume: 884.007 nm^3, corresponds to roughly 397800 electrons<br>No velocities found<br> system size : 9.205 8.440 11.378 (nm)<br>
diameter : 12.498 (nm)<br> center : 6.524 6.242 9.385 (nm)<br> box vectors : 9.205 8.440 11.378 (nm)<br> box angles : 90.00 90.00 90.00 (degrees)<br> box volume : 884.01 (nm^3)<br>
shift : 3.226 3.508 -4.789 (nm)<br>new center : 9.750 9.750 4.596 (nm)<br>new box vectors : 13.000 13.000 13.000 (nm)<br>new box angles : 60.00 60.00 90.00 (degrees)<br>new box volume :1553.51 (nm^3)<br>
<br><br>## Last line of the output .gro file:<br> 13.00000 13.00000 9.19239 0.00000 0.00000 0.00000 0.00000 6.50000 6.50000<br><br>## g_mindist output:<br><br>Last frame 0 time 2.000 <br><br>
The shortest periodic distance is 1.5735 (nm) at time 2 (ps),<br>between atoms 992 and 8506<br><br><br>##<br>## Protein Orientation 2 editconf_4.5.5 output:<br>##<br><br>Read 17463 atoms<br>Volume: 996.803 nm^3, corresponds to roughly 448500 electrons<br>
No velocities found<br> system size : 12.299 9.828 8.247 (nm)<br> diameter : 12.498 (nm)<br> center : 5.898 4.759 8.713 (nm)<br> box vectors : 12.299 9.828 8.247 (nm)<br> box angles : 90.00 90.00 90.00 (degrees)<br>
box volume : 996.80 (nm^3)<br> shift : 3.852 4.991 -4.117 (nm)<br>new center : 9.750 9.750 4.596 (nm)<br>new box vectors : 13.000 13.000 13.000 (nm)<br>new box angles : 60.00 60.00 90.00 (degrees)<br>
new box volume :1553.51 (nm^3)<br><br>## Last line of the output .gro file:<br> 13.00000 13.00000 9.19239 0.00000 0.00000 0.00000 0.00000 6.50000 6.50000<br><br>## g_mindist output:<br><br>Last frame 0 time 2.000 <br>
<br>The shortest periodic distance is 2.59235 (nm) at time 2 (ps),<br>between atoms 3915 and 6814<br><br><br><br>Thanks in advance,<br>Thomas<br><br><br><div class="gmail_quote">On 26 April 2012 15:36, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hey Thomas,<br>
<br>
The rhombic dodecahedron corresponds to the packing of a sphere.<br>
Consequently, the difference in the distance between periodic images<br>
over the shortest diameter and the longest diameter is pretty small.<br>
That means that there isn't really an optimal orientation in a rhombic<br>
dodecahedron; all orientations are pretty much equal. And that's how<br>
it should be :)<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div class="h5"><br>
On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>> wrote:<br>
> Dear GROMACS users,<br>
><br>
> I have noticed that for constant box dimensions the minimum distance from<br>
> the periodic images of a protein depends on the initial orientation of the<br>
> protein, whereas the orientation of the dodecahedron relative to the x,y,z<br>
> axes remains fixed. These are the command lines I use:<br>
><br>
> pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff<br>
> amber99sb-ildn -water tip3p -ignh<br>
> # set the new dodecahedron box dimensions<br>
> editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro<br>
> # solvate with TIP3P<br>
> genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p<br>
> protein.top<br>
> # add ions<br>
> grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o<br>
> protein_ions.tpr<br>
> echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top<br>
> -pname NA -nname CL -np 3<br>
><br>
> grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o<br>
> protein_EM.tpr<br>
> mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM<br>
><br>
> # to see a dodecahedron<br>
> echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s<br>
> protein_EM.tpr -o em_dodecahedron.xtc<br>
> # measure the minimum distance from the periodic images<br>
> echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi<br>
><br>
><br>
> Is there any way to optimize the orientation of protein inside the<br>
> dodecahedron in order to get the maximum possible mindist?<br>
><br>
><br>
> Thanks in advance,<br>
> Thomas<br>
><br clear="all"><br></div></div></blockquote></div><br>-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>
</div>