RE: protein movement

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Sep 29 2019 - 16:32:03 CDT

The configuration file you've written is telling colvars to constrain the movement of the protein relative to the protein itself (main and ref refer to the same atoms). Since this is tautological, the colvar doesn't do anything. I suggest you look into making ref a dummy atom at the origin.

-Josh

On 2019-09-29 14:06:01-06:00 owner-namd-l_at_ks.uiuc.edu 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

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