[gmx-users] walp lipids around protein in membrane protein simulation
mark.j.abraham at gmail.com
Thu Oct 22 09:55:57 CEST 2015
If the protein has rotated with respect to the bilayer over time, then you
cannot rotate a simulation frame to align simultaneously the bilayer with
the bilayer and the protein with the protein.
On Thu, Oct 22, 2015 at 8:58 AM 凌未风 <grx1985 at qq.com> wrote:
> 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
> 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
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