[gmx-users] walp lipids around protein in membrane protein simulation
grx1985 at qq.com
Thu Oct 22 08:58:05 CEST 2015
I am running a membrane protein simulation, in which the protein is inserted into a membrane bilayer.
During my simulations, the protein rotate and diffuse on the bilayer plane. I am trying to put the protein in the center of the bilayer and align the protein with the initial conformation.
I did the following things to put the protein in the center of the bilayer: trjconv -s *.tpr -f *.xtc -center -pbc whole -o *.xtc
However, when I tried to align the protein with the initial conformation by the following command: trjconv -s *.tpr -f *.xtc -fit rot+trans -o *.xtc
In the output trajectory, the protein is at the center of the bilayer and aligned with the initial conformation, but the x and y axis of the bilayer is not consistent with the initial conformation, i.e., the bilayer rotated on the xy plane.
I understand this is because I aligned the protein to the initial conformation.
My question is: is there any way to put the protein at the center of bilayer and align the protein to the initial conformation while still keep the x and y axes of the bilayer consistent with the initial structure?
Thanks very much. I really appreciate for any help.
With my best regards,
University of Calgary
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