This is part of the generic module

This action is used to align a molecule to a template.

This can be used to move the coordinates stored in plumed so as to be aligned with a provided template in PDB format. Pdb should contain also weights for alignment (see the format of PDB files used e.g. for RMSD). Make sure your PDB file is correclty formatted as explained in this page. Weights for displacement are ignored, since no displacement is computed here. Notice that all atoms (not only those in the template) are aligned. To see what effect try the DUMPATOMS directive to output the atomic positions.

Also notice that PLUMED propagate forces correctly so that you can add a bias on a CV computed after alignment. For many CVs this has no effect, but in some case the alignment can change the result. Examples are:

  • POSITION CV since it is affected by a rigid shift of the system.
  • DISTANCE CV with COMPONENTS. Since the alignment could involve a rotation (with TYPE=OPTIMAL) the actual components could be different from the original ones.
  • CELL components for a similar reason.
  • DISTANCE from a FIXEDATOM, provided the fixed atom is introduced after the FIT_TO_TEMPLATE action.
The implementation of TYPE=OPTIMAL is available but should be considered in testing phase. Please report any strange behavior.
This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. As a general rule, put it at the top of the input file. Also, unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.
The molecule used for alignment should be whole. In case it is broken by the host MD code, please use WHOLEMOLECULES to reconstruct it before FIT_TO_TEMPLATE .
Compulsory keywords
STRIDE ( default=1 ) the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!
REFERENCE a file in pdb format containing the reference structure and the atoms involved in the CV.
TYPE ( default=SIMPLE ) the manner in which RMSD alignment is performed. Should be OPTIMAL or SIMPLE.

Align the atomic position to a template then print them. The following example is only translating the system so as to align the center of mass of a molecule to the one in the reference structure ref.pdb:

# dump coordinates before fitting, to see the difference:

# fit coordinates to ref.pdb template
# this is a "TYPE=SIMPLE" fit, so that only translations are used.

# dump coordinates after fitting, to see the difference:

The following example instead performs a rototranslational fit.

# dump coordinates before fitting, to see the difference:

# fit coordinates to ref.pdb template
# this is a "TYPE=OPTIMAL" fit, so that rototranslations are used.

# dump coordinates after fitting, to see the difference:

In the following example you see two completely equivalent way to restrain an atom close to a position that is defined in the reference frame of an aligned molecule. It could be for instance the center of mass of a ligand with respect to a protein

# center of the ligand:
ce: CENTER ATOMS=100-110


# place a fixed atom in the protein reference coordinates:
fix: FIXEDATOM AT=1.0,1.1,1.0

# take the distance between the fixed atom and the center of the ligand

# apply a restraint

Notice that you could have obtained an (almost) identical result adding a fictitious atom to ref.pdb with the serial number corresponding to the ce atom (there is no automatic way to get it, but in this example it should be the number of atoms of the system plus one), and properly setting the weights for alignment and displacement in RMSD. There are two differences to be expected: (ab) FIT_TO_TEMPLATE might be slower since it has to rototranslate all the available atoms and (b) variables employing PBCs (such as DISTANCE without NOPBC, as in the example above) are allowed after FIT_TO_TEMPLATE, whereas RMSD expects PBCs to be already solved. The latter means that before the RMSD statement one should use WRAPAROUND or WHOLEMOLECULES to properly place the ligand.