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

[Thomas Evangelidis]

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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