Shortcut: DRMSD

Module	colvar
Description	Usage
Calculate the distance RMSD with respect to a reference structure.
output value	type
the DRMSD distance between the instantaneous structure and the reference structure	scalar/vector

Further details and examples

Calculate the distance RMSD with respect to a reference structure.

To calculate the root-mean-square deviation between the atoms in two configurations you must first superimpose the two structures in some ways. Obviously, it is the internal vibrational motions of the structure - i.e. not the translations and rotations - that are interesting. However, aligning two structures by removing the translational and rotational motions is not easy. Furthermore, in some cases there can be alignment issues caused by so-called frame-fitting problems. It is thus often easier to calculate the distances between all the pairs of atoms. The distance between the two structures, ${\bf X}^a$ and ${\bf X}^b$ can then be measured as:

$$d({\bf X}^A, {\bf X}^B) = \sqrt{\frac{1}{N(N-1)} \sum_{i \ne j} [ d({\bf x}_i^a,{\bf x}_j^a) - d({\bf x}_i^b,{\bf x}_j^b) ]^2}$$

where $N$ is the number of atoms and $d({\bf x}_i,{\bf x}_j)$ represents the distance between atoms $i$ and $j$. Clearly, this representation of the configuration is invariant to translation and rotation. However, it can become expensive to calculate when the number of atoms is large. This can be resolved within the DRMSD colvar by setting LOWER_CUTOFF and UPPER_CUTOFF. These keywords ensure that only pairs of atoms that are within a certain range are incorporated into the above sum.

In PDB files the atomic coordinates and box lengths should be in Angstroms unless you are working with natural units. If you are working with natural units then the coordinates should be in your natural length unit. Click here for more details on the PDB file format.

Examples

The following tells plumed to calculate the distance RMSD between the positions of the atoms in the reference file and their instantaneous position. Only pairs of atoms whose distance in the reference structure is within 0.1 and 0.8 nm are considered.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt-drmsd/test1.pdb
DRMSDCalculate the distance RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt-drmsd/test1.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt-drmsd/test1.pdb
    
ATOM      2  O   ALA     2      -0.926  -2.447  -0.497  1.00  1.00      DIA  O
ATOM      4  HNT ALA     2       0.533  -0.396   1.184  1.00  1.00      DIA  H
ATOM      6  HT1 ALA     2      -0.216  -2.590   1.371  1.00  1.00      DIA  H
ATOM      7  HT2 ALA     2      -0.309  -1.255   2.315  1.00  1.00      DIA  H
  
 LOWER_CUTOFFonly pairs of atoms further than LOWER_CUTOFF are considered in the calculation=0.1 UPPER_CUTOFFonly pairs of atoms closer than UPPER_CUTOFF are considered in the calculation=0.8

The following tells plumed to calculate a DRMSD value for a pair of molecules.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt-drmsd/test0.pdb
DRMSDCalculate the distance RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt-drmsd/test0.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt-drmsd/test0.pdb
    
ATOM      2  O   ALA     2      -0.926  -2.447  -0.497  1.00  1.00      DIA  O
ATOM      4  HNT ALA     2       0.533  -0.396   1.184  1.00  1.00      DIA  H
ATOM      6  HT1 ALA     2      -0.216  -2.590   1.371  1.00  1.00      DIA  H
ATOM      7  HT2 ALA     2      -0.309  -1.255   2.315  1.00  1.00      DIA  H
TER
ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
ATOM     16  HN  ALA     2       1.713   1.021  -0.873  1.00  1.00      DIA  H
TER
  
 LOWER_CUTOFFonly pairs of atoms further than LOWER_CUTOFF are considered in the calculation=0.1 UPPER_CUTOFFonly pairs of atoms closer than UPPER_CUTOFF are considered in the calculation=0.8 TYPE what kind of DRMSD would you like to calculate=INTER-DRMSD

Notice that in the input reference file (which you can see by clicking on regtest/basic/rt-drmsd/test0.pdb ) the atoms in each of the two molecules are separated by a TER command as shown below.

In this example the INTER-DRMSD type ensures that the set of distances from which the final quantity is computed involve one atom from each of the two molecules. If this is replaced by INTRA-DRMSD then only those distances involving pairs of atoms that are both in the same molecule are computed.

Syntax

The following table describes the keywords and options that can be used with this action