[gmx-users] walp lipids around protein in membrane protein simulation

[凌未风]

Hi All:

    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, 
    Ruo-Xu Gu
    University of Calgary