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

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
dThe DRMSD action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DRMSD distance between the instantaneous structure and the reference structure: DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut and it has hidden defaults. 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
...
d: DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut and uses the defaults shown here. 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
 TYPE what kind of DRMSD would you like to calculate=DRMSD
...
# PLUMED interprets the command:
# d: DRMSD ...
#   REFERENCE=regtest/basic/rt-drmsd/test1.pdb
#   LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
# ...
# as follows (Click the red comment above to revert to the short version of the input):
d_dThe DISTANCE action with label d_d calculates the following quantities:
 Quantity   
 Type   
 Description  
d_d
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=2,4 ATOMS2the pair of atom that we are calculating the distance between=2,6 ATOMS3the pair of atom that we are calculating the distance between=2,7 ATOMS4the pair of atom that we are calculating the distance between=4,6 ATOMS5the pair of atom that we are calculating the distance between=4,7     # Action input conctinues with 1 further ATOMSn keywords, 
d_refThe CONSTANT action with label d_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.302672,0.200349,0.311591,0.232586,0.165106,0.163768
d_diffsThe CUSTOM action with label d_diffs calculates the following quantities:
 Quantity   
 Type   
 Description  
d_diffs
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_d,d_ref FUNCthe function you wish to evaluate=(x-y)*(x-y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d_uThe SUM action with label d_u calculates the following quantities:
 Quantity   
 Type   
 Description  
d_u
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=d_diffs PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d_2The CUSTOM action with label d_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d_2
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_u FUNCthe function you wish to evaluate=(x/6) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dThe CUSTOM action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 

The following tells plumed to calculate the square of the 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
dThe DRMSD action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DRMSD distance between the instantaneous structure and the reference structure: DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut. 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
  SQUARED This should be setted if you want MSD instead of RMSD 
...
# PLUMED interprets the command:
# d: DRMSD ...
#   REFERENCE=regtest/basic/rt-drmsd/test0.pdb
#   LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
#   SQUARED
# ...
# as follows (Click the red comment above to revert to the short version of the input):
d_dThe DISTANCE action with label d_d calculates the following quantities:
 Quantity   
 Type   
 Description  
d_d
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMS1the pair of atom that we are calculating the distance between=12,2 ATOMS2the pair of atom that we are calculating the distance between=12,4 ATOMS3the pair of atom that we are calculating the distance between=12,6 ATOMS4the pair of atom that we are calculating the distance between=12,7 ATOMS5the pair of atom that we are calculating the distance between=14,2     # Action input conctinues with 7 further ATOMSn keywords, 
d_refThe CONSTANT action with label d_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.522074,0.415229,0.596097,0.541499,0.341802,0.303466,0.43294,0.403465,0.43741,0.276252,0.466861,0.440817
d_diffsThe CUSTOM action with label d_diffs calculates the following quantities:
 Quantity   
 Type   
 Description  
d_diffs
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_d,d_ref FUNCthe function you wish to evaluate=(x-y)*(x-y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d_uThe SUM action with label d_u calculates the following quantities:
 Quantity   
 Type   
 Description  
d_u
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=d_diffs PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dThe CUSTOM action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_u FUNCthe function you wish to evaluate=x/12 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 

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.

Periodic boundary conditions

Notice that PLUMED does not use periodic boundary conditions when computing the reference distances. However, the instantaneous values of the distances are computed using periodic boundary conditions. If you would like not to use periodic boundary conditions when computing these instaneous distances you use the NOPBC flag as illustrated below:

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

#SETTINGS INPUTFILES=regtest/basic/rt-drmsd/test1.pdb
dThe DRMSD action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DRMSD distance between the instantaneous structure and the reference structure: DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut and it has hidden defaults. 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 NOPBC ignore the periodic boundary conditions when calculating distances
...
d: DRMSDCalculate the distance RMSD with respect to a reference structure. This action is a shortcut and uses the defaults shown here. 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 NOPBC ignore the periodic boundary conditions when calculating distances
 TYPE what kind of DRMSD would you like to calculate=DRMSD
...
# PLUMED interprets the command:
# d: DRMSD ...
#   REFERENCE=regtest/basic/rt-drmsd/test1.pdb
#   LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 NOPBC
# ...
# as follows (Click the red comment above to revert to the short version of the input):
d_dThe DISTANCE action with label d_d calculates the following quantities:
 Quantity   
 Type   
 Description  
d_d
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=2,4 ATOMS2the pair of atom that we are calculating the distance between=2,6 ATOMS3the pair of atom that we are calculating the distance between=2,7 ATOMS4the pair of atom that we are calculating the distance between=4,6 ATOMS5the pair of atom that we are calculating the distance between=4,7     # Action input conctinues with 1 further ATOMSn keywords, 
d_refThe CONSTANT action with label d_ref calculates the following quantities:
 Quantity   
 Type   
 Description  
d_ref
vector
the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.302672,0.200349,0.311591,0.232586,0.165106,0.163768
d_diffsThe CUSTOM action with label d_diffs calculates the following quantities:
 Quantity   
 Type   
 Description  
d_diffs
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_d,d_ref FUNCthe function you wish to evaluate=(x-y)*(x-y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d_uThe SUM action with label d_u calculates the following quantities:
 Quantity   
 Type   
 Description  
d_u
scalar
the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details ARGthe vector/matrix/grid whose elements shuld be added together=d_diffs PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d_2The CUSTOM action with label d_2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d_2
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_u FUNCthe function you wish to evaluate=(x/6) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dThe CUSTOM action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d_2 FUNCthe function you wish to evaluate=sqrt(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- 

Full list of keywords

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

Keyword	Type	Default	Description
REFERENCE	compulsory	none	a file in pdb format containing the reference structure and the atoms involved in the CV
TYPE	compulsory	DRMSD	what kind of DRMSD would you like to calculate
LOWER_CUTOFF	optional	not used	only pairs of atoms further than LOWER_CUTOFF are considered in the calculation
UPPER_CUTOFF	optional	not used	only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation
SQUARED	optional	false	This should be setted if you want MSD instead of RMSD
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances

deprecated keywords

The keywords in the following table can still be used with this action but have been deprecated

Keyword	Description
NUMERICAL_DERIVATIVES	Including this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only