Re: How to remove center of mass translation of macromolecule

From: Teerapong Pirojsirikul (tpirojsi_at_ucsd.edu)
Date: Thu Jun 13 2013 - 17:38:07 CDT

Hi Jerome,

Thank you very much for your advice. I have tried both approaches out. For
the first suggestion, I have plotted the rmsd of the COM of the RNA
backbone and the values were running around 0.1. Together with rotation
blocking, I could remove both translation and rotation of the RNA.

As for the second approach, as I understand, the MD simulation is performed
regularly, which is there might be rotation and translation of the RNA, but
the colvar output will return the distance vector between the ion and, in
the case of your input file, dummy atom at position (0,0,0) in the frame of
reference defined in group1, isn't it?

I first tried out with this input colvar file,

colvar {
  name ionPosition
  distanceVec {
      group1 {
          atomNumbers 2020
      }
      group2 {
         dummyAtom (0.0, 0.0, 0.0)
      }
  }
}

The initial position of Mg from PDB file used to start the simulation is
(37.129, 36.890, 33.701) But the first few lines from colvar traj I got are
# step ionPosition

           0 ( 3.09493954130363e+01 , 2.31730595523354e+01 ,
-3.37012114861363e+01 )
        1000 ( 3.11665756227577e+01 , 2.32411814446486e+01 ,
-3.36415457741733e+01 )
        2000 ( 3.09509987444541e+01 , 2.28119750757673e+01 ,
-3.34979393701572e+01 )
..

What is wondering me is why at the step 0, the distance vector returned
different values from the initial position in PDB file. I also extracted
the Mg postions at other time steps from the dcd file and they didn't seem
to be in agreement with the colvar trajectory output as well. If the
coordinates in a pdb file typically refer to the origin at (0, 0, 0), I
think both outputs should result the same thing.

Please correct me if I'm wrong.

Best,
Tee

2013/6/12 Jrme Hnin <jerome.henin_at_ibpc.fr>

> 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
>

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