Re: protein movement

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Sep 30 2019 - 07:11:08 CDT

Hello Mehdi, you are restraining the relative distance between two
subunits, which disregards all translations. To restrain the distance from
a specific position, one of the group should be a dummyAtom located at that
same position.

Giacomo

On Sun, Sep 29, 2019 at 4:00 PM Mahdi Mousaei <mahdi.mousaei_at_ucalgary.ca>
wrote:

> Hello to all,
>
> I want to fix my protein in the bilayer in XY plane, for this purpose the
> cylindrical constrain applied to prevent protein movement in XY direction
> and at the same time give some space to protein to have its movement. I
> wrote the colvars like this:
>
> colvar {
> lowerboundary -1.0
> upperboundary 5.0
> upperWall 3.0;
> upperwallconstant 10
>
> name lateral
> distanceXY {
> main {
>
> atomsFile ref.pdb #CA atoms of helix of protein
>
> atomsCol B
>
> atomsColValue 1.00
>
> }
> ref {
> atomsFile ref.pdb
>
> atomsCol B
>
> atomsColValue 1.00
> }
> axis {(0.0, 0.0, 1.0)}
> forceNoPBC yes
> }
> }
>
> Unfortunately, it seems that it is not working since the protein is moving
> in XY plane. It would be great if I could hear your comments and suggestion
> how to fix this problem.
> Thank you :)
>
> Best Wishes,
> Mehdi
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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