I have simulated a protein-lipid system as cg with gromacs. Before running , 10 proteins were placed on top of the membrane with the gmx insert command. I checked PDBs. All were right. The simulation was run for 1.5 µs. At the end, PBC was removed in different ways. For example, the following steps were run.
gmx trjconv -f production.xtc -s production.tpr -o production_whole.xtc -pbc whole
gmx trjconv -f production_whole.xtc -s production.tpr -o production_whole_nojump.xtc -pbc nojump
gmx trjconv -f production_whole_nojump.xtc -s production.tpr -o production_whole_nojump_center.xtc -pbc mol -center -n index.ndx
Finally, the structure result from last frame was checked, The result showed that some peptids are placed in inner and some in the outer part of membrane. I think it's because of the rotation. But with the following command, I could not remove rotaion
gmx trjconv -f production_whole.xtc -s production.tpr -o production_whole_nojump.xtc -fit rotatexy
So any one have suggestion to remove rotation? It is appreciated for any help.
The 3D representation of lipid-protein from last frame have been attached.
If the proteins are not embedded in the lipid bilayer, that is, they are in some way kept in place, they will -to some extent- diffuse around in the water box.
Are PBC on in all directions? And do you have only one lipid bilayer? In that case you have no outer/inner, since a protein can leave the box from the top side and re-enter from the bottom side.
Dear Nicola
Thanks your reply.
Yes. PBC are in all direction and i have only 1 lipid bilayer. The lipid bilayer is not symmetric. Outer part in bilayer is a part in which is exposure to surrounding medium.
You are right. A part of a protein has left the box from top an has re-entered from the bottom according to the PBC state. Now my problem is about removing the PBC.
Dear Javad Zamani
What do you mean with removing PBC? If you want to remove them visually, you can do it with gromacs tool gmx trjconv.
However, there is no outer or inner side. The two sides are not symmetric, but because of PBC they are exposed to the same medium.
Best,
Nicola
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