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

Mark Abraham 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
> 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
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