MULTI_RMSD
This is part of the colvar module

Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure.

When you have large proteins the calculation of the root mean squared deviation between all the atoms in a reference structure and the instantaneous configuration becomes prohibitively expensive. You may thus instead want to calculate the RMSD between the atoms in a set of domains of your protein and your reference structure. That is to say:

\[ d(X,X_r) = \sqrt{ \sum_{i} w_i\vert X_i - X_i' \vert^2 } \]

where here the sum is over the domains of the protein, \(X_i\) represents the positions of the atoms in domain \(i\) in the instantaneous configuration and \(X_i'\) is the positions of the atoms in domain \(i\) in the reference configuration. \(w_i\) is an optional weight.

The distances for each of the domains in the above sum can be calculated using the DRMSD or RMSD measures or using a combination of these distance. The reference configuration is specified in a pdb file like the one below:

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
ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  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
ATOM     18  HA  ALA     2       0.099  -0.774  -2.218  1.00  1.00      DIA  H
ATOM     19  CB  ALA     2       2.063  -1.223  -1.276  1.00  1.00      DIA  C
ATOM     20  HB1 ALA     2       2.670  -0.716  -2.057  1.00  1.00      DIA  H
ATOM     21  HB2 ALA     2       2.556  -1.051  -0.295  1.00  1.00      DIA  H
ATOM     22  HB3 ALA     2       2.070  -2.314  -1.490  1.00  1.00      DIA  H
END

with the TER keyword being used to separate the various domains in you protein.

Examples

The following tells plumed to calculate the RMSD distance between the positions of the atoms in the reference file and their instantaneous position. The Kearsley algorithm for each of the domains.

Click on the labels of the actions for more information on what each action computes
tested on v2.9
MULTI_RMSD 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV. 
=file1.pdb 
TYPE
compulsory keyword ( default=MULTI-SIMPLE )
the manner in which RMSD alignment is performed. 
=MULTI-OPTIMAL

The following tells plumed to calculate the RMSD distance between the positions of the atoms in the domains of reference the reference structure and their instantaneous positions. Here distances are calculated using the DRMSD measure.

Click on the labels of the actions for more information on what each action computes
tested on v2.9
MULTI_RMSD 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV. 
=file1.pdb 
TYPE
compulsory keyword ( default=MULTI-SIMPLE )
the manner in which RMSD alignment is performed. 
=MULTI-DRMSD

in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax: 

NOPBC to calculate distances without PBC
LOWER_CUTOFF=# only pairs of atoms further than LOWER_CUTOFF are considered in the calculation
UPPER_CUTOFF=# only pairs of atoms further than UPPER_CUTOFF are considered in the calculation

as shown in the following example

REMARK NOPBC
REMARK LOWER_CUTOFF=0.1
REMARK UPPER_CUTOFF=0.8
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
ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  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
ATOM     18  HA  ALA     2       0.099  -0.774  -2.218  1.00  1.00      DIA  H
ATOM     19  CB  ALA     2       2.063  -1.223  -1.276  1.00  1.00      DIA  C
ATOM     20  HB1 ALA     2       2.670  -0.716  -2.057  1.00  1.00      DIA  H
ATOM     21  HB2 ALA     2       2.556  -1.051  -0.295  1.00  1.00      DIA  H
ATOM     22  HB3 ALA     2       2.070  -2.314  -1.490  1.00  1.00      DIA  H
END
Glossary of keywords and components
Compulsory keywords
REFERENCE a file in pdb format containing the reference structure and the atoms involved in the CV.
TYPE ( default=MULTI-SIMPLE ) the manner in which RMSD alignment is performed. Should be MULTI-OPTIMAL, MULTI-OPTIMAL-FAST, MULTI-SIMPLE or MULTI-DRMSD.
Options
NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically
NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances
SQUARED

( default=off ) This should be set if you want the mean squared displacement instead of the root mean squared displacement