Dear GROMACS users,<br><br>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:<br>
<br>pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff 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 protein.top<br># add ions<br>grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o protein_ions.tpr<br>echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top -pname NA -nname CL -np 3 <br>
<br>grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o 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 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 dodecahedron in order to get the maximum possible mindist?<br>
<br><br>Thanks in advance,<br>Thomas<br><br><br clear="all"><br>-- <br>
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<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>
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