Action: SECONDARY_STRUCTURE_DRMSD

Module	secondarystructure
Description	Usage
Calclulate the DRMSD between segments of a protein and a reference structure of interest

Details and examples

Calclulate the DRMSD between segments of a protein and a reference structure of interest

This action is used in the shortcuts ALPHARMSD, ANTIBETARMSD and PARABETARMSD. It calculates a vector of DRMSD values between a single reference multiple configurations and the instantaneous positions of various groups of atoms. For example, in the following input we define a single set of reference set of coordinates for 3 atoms.

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

c1The SECONDARY_STRUCTURE_DRMSD action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 vector the value calculated by this action: SECONDARY_STRUCTURE_DRMSDCalclulate the DRMSD between segments of a protein and a reference structure of interest More details ...
    ATOMSthis is the full list of atoms that we are investigating=13-24
    BONDLENGTH the length to use for bonds=0.17 STRUCTURE1the reference structure=1,0,0,0,1,0,0,0,1
    SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2 SEGMENT2this is the lists of atoms in the segment that are being considered=3,4,5
    SEGMENT3this is the lists of atoms in the segment that are being considered=6,7,8 SEGMENT4this is the lists of atoms in the segment that are being considered=9,10,11
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1 FILEthe name of the file on which to output these quantities=colvar

A four dimensional vector is then returned that contains the DRMSD distances between the 4 sets of 3 atoms that were specified using the SEGMENT keywords and the reference coordinates. Notice that you can use multiple instances of the STRUCTURE keyword. In general the the number of vectors output is equal to the number of times the STRUCTURE keyword is used. Further note that the indices specified to the SEGMENT keywords give the indices in the list of atoms specified by the ATOMS keyword. SEGMENT1=0,1,2 in the above input is measuring the distance between the instaneous positions of atoms 13, 14 and 15 and the reference structure.

Periodic boundary conditions

If you turn off periodic boundary conditions by using the NOPBC flag as shown below:

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

c1The SECONDARY_STRUCTURE_DRMSD action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 vector the value calculated by this action: SECONDARY_STRUCTURE_DRMSDCalclulate the DRMSD between segments of a protein and a reference structure of interest More details ...
    ATOMSthis is the full list of atoms that we are investigating=13-24 NOPBC ignore the periodic boundary conditions
    BONDLENGTH the length to use for bonds=0.17 STRUCTURE1the reference structure=1,0,0,0,1,0,0,0,1
    SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2 SEGMENT2this is the lists of atoms in the segment that are being considered=3,4,5
    SEGMENT3this is the lists of atoms in the segment that are being considered=6,7,8 SEGMENT4this is the lists of atoms in the segment that are being considered=9,10,11
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=c1 FILEthe name of the file on which to output these quantities=colvar

the distances between in the instaneous structure are evaluated in a way that does not take the periodic boundary conditions into account. Whenver this flag is not present the distances in the instaneous structure are evaluated in a way that takes the periodic boundary conditions into account.

If you use the ALIGN_STRANDS flag to evaluate the distances in a way that takes the periodic boundary conditions into accounts means that calculating the distance between the positions of the 7th and 22nd atoms ( $\mathbf{x}_7$ and $\mathbf{x}_{22}$ ) of the instanenous structures using the periodic boundary conditions. The 22 atom is the repositioned at:

$\mathbf{x}_{22} = \mathbf{x}_7 + ( \mathbf{x}_{22} - \mathbf{x}_7 )$

where the difference in the second term on the right of the equality sign is evaluated using the periodic boundary conditions. New positions are then determined for atoms 16 through 30 by adding the difference (evaluated without PBC) between the new position for atom 22 after the above transformation has been perfomed and the original position of this atom. This treatment is designed for making sure that the two strands of the ANTIBETARMSD and PARABETARMSD sheets are not broken by the periodic boundaries.

Working with beta sheet like structures

As discussed in the documentation for ANTIBETARMSD and PARABETARMSD using the STRANDS_KEYWORD cutoff can speed up the calculation dramatically. The reason this keyword gives such dramatric speed ups is illustrated by the example input:

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

ab_cut_distsThe DISTANCE action with label ab_cut_dists calculates the following quantities: Quantity    Type    Description  
ab_cut_dists 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=19,69 ATOMS2the pair of atom that we are calculating the distance between=19,79
  ATOMS3the pair of atom that we are calculating the distance between=19,89 ATOMS4the pair of atom that we are calculating the distance between=19,99
  ATOMS5the pair of atom that we are calculating the distance between=19,109
...
ab_cutThe CUSTOM action with label ab_cut calculates the following quantities: Quantity    Type    Description  
ab_cut 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=ab_cut_dists FUNCthe function you wish to evaluate=step(1-x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ab_rmsdThe SECONDARY_STRUCTURE_DRMSD action with label ab_rmsd calculates the following quantities: Quantity    Type    Description  
ab_rmsd vector the value calculated by this action: SECONDARY_STRUCTURE_DRMSDCalclulate the DRMSD between segments of a protein and a reference structure of interest More details ...
   BONDLENGTH the length to use for bonds=0.17 ALIGN_STRANDS ensure that the two halves of a beta sheet are not broken by the periodic boundaries before doing alignment MASKa vector which is used to determine which elements of the secondary structure variable should be computed=ab_cut
   ATOMSthis is the full list of atoms that we are investigating=7,9,11,15,16,17,19,21,25,26,27,29,31,35,36,37,39,41,45,46,47,49,51,55,56,57,59,61,65,66,67,69,71,75,76,77,79,81,85,86,87,89,91,95,96,97,99,101,105,106,107,109,111,115,116,117,119,121,125,126
   SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39
   SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44
   SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49
   SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54
   SEGMENT5this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59
   STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102
...
ab_ltuThe LESS_THAN action with label ab_ltu calculates the following quantities: Quantity    Type    Description  
ab_ltu vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=ab_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12} MASKthe label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed=ab_cut
ab_ltThe CUSTOM action with label ab_lt calculates the following quantities: Quantity    Type    Description  
ab_lt 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=ab_ltu,ab_cut FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
abThe SUM action with label ab calculates the following quantities: Quantity    Type    Description  
ab 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=ab_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab FILEthe name of the file on which to output these quantities=colvar

The input above illustrates the input that is used by the shortcut that computes the ANTIBETARMSD. You can see that the distances between the atoms on the two strands of the beta sheet are computed in a DISTANCE action before we computed the SECONDARY_STRUCTURE_DRMSD values. These distances are then transformed by a Heavyside function that is 1 if the distance is less than 1 nm and zero otherwise. This vector of ones and zeros is then fed into the SECONDARY_STRUCTURE_DRMSD action as a mask. By doing this we ensure that SECONDARY_STRUCTURE_DRMSD values are only computed for parts of the strand that are close together. This avoids performing unecessarily expensive calculations and is also a reasonable thing to do as if the two strands are more than 1 nm appart the residues in question are not at all similar to a beta sheet structure.

Input

The arguments and atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
MASK	vector	a vector which is used to determine which elements of the secondary structure variable should be computed
ATOMS	atoms	this is the full list of atoms that we are investigating

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Description
struct	scalar	the vectors containing the rmsd distances between the residues and each of the reference structures
lessthan	scalar	the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold

Full list of keywords

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

Keyword	Type	Default	Description
MASK	input	none	a vector which is used to determine which elements of the secondary structure variable should be computed
ATOMS	input	none	this is the full list of atoms that we are investigating
BONDLENGTH	compulsory	0.17	the length to use for bonds
SERIAL	optional	false	do the calculation in serial. Further information about this flag can be found here.
USEGPU	optional	false	run this calculation on the GPU. Further information about this flag can be found here.
NOPBC	optional	false	ignore the periodic boundary conditions
SEGMENT	optional	not used	this is the lists of atoms in the segment that are being considered
STRUCTURE	optional	not used	the reference structure
ALIGN_STRANDS	optional	false	ensure that the two halves of a beta sheet are not broken by the periodic boundaries before doing alignment

References

More information about how this action can be used is available in the following articles:

F. Pietrucci, A. Laio, A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. Journal of Chemical Theory and Computation. 5, 2197–2201 (2009)

Quantity	Type	Description
c1	vector	the value calculated by this action