Re: How to remove center of mass translation of macromolecule

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jun 12 2013 - 04:00:48 CDT

Hi Tee,

The simplest way to restrain the translations of the RNA molecule is to restrain a distance coordinate linking its center of mass to a dummy atom (that is, a fixed point). The input for that restraint would be:

colvar {
  name RNAcenterDistance

  distance {
    group1 {
      atomNumbers 1 2 3 4 5 # RNA reference atoms
    }
    group2 {
      dummyAtom (42.0, 42.0, -42.0) # set to initial position of group1 center
    }
  }
}

harmonic {
  colvars RNAcenterDistance

  centers 0.0
  forceConstant 10.0
}

Note that if you use the colvars module, you might also be able to do your calculation without restraining the RNA molecule at all, neither its translation nor its rotation. You can do that by measuring the coordinate of interest (here the 3D position of the ion as a distanceVec coordinate) in a frame of reference linked to the RNA, that is, rotated and translated to match global motion of the RNA molecule. The complete input would then look like this:

colvar {
  name ionPosition

  distanceVec {

    group1 {
      atomNumbers 4242 # ion
    
      centerReference # use relative coordinates
      rotateReference # (translated and rotated frame of reference)
      refPositionsGroup { # work in frame of reference based on RNA molecule
        atomsFile ref.pdb # from separate file
        atomsCol B # RNA reference atoms tagged in column B
      }
      refPositionsFile ref.pdb # initial coordinates for reference group
    }

    group2 {
      dummyAtom (0.0, 0.0, 0.0) # arbitrary reference point for the ion position
    }
  }
}

The second group could also be a group of atoms within the RNA molecule, defining the active site - in that case, group2 should be calculated in the same local reference frame (re-using the options centerReference, refPositionsGroup, etc.)

Cheers,
Jerome

----- Original Message -----
>
> Hi NAMD users,
>
>
> I have been looking for how to remove center of mass translation of a
> macromolecule. I have read many threads regarding this issue in the
> mailing list but still got confused. I'm working on a sampling
> problem and want to reconstruct a free energy surface as a function
> of Cartesian coordinates (x,y, and z) of a certain ion moving in an
> active site of an RNA molecule. As a result, I need to perform the
> MD simulation at a fix orientation (by removing rotation and
> translation of the RNA). I can successfully fix the rotation by
> blocking the backbone of the molecule using orientation colvar
> module. But I'm wondering what is the easiest way to remove the
> translation of the RNA. I have tried fixing one atom but am curious
> whether this will cause any artificial dynamics to my system or to
> the fixed atom. Also I have seen many people talking about dummy
> atom but don't quite have a clear idea how to make use of it. Any
> advice would be appreciated.
>
>
> Tee

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:20 CST