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| 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.
| 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. |
| 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 |
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.
MULTI_RMSD REFERENCE=file.pdb TYPE=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.
MULTI_RMSD REFERENCE=file.pdb TYPE=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
1.8.14