protein movement

From: Mahdi Mousaei (mahdi.mousaei_at_ucalgary.ca)
Date: Sun Sep 29 2019 - 14:58:30 CDT

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

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