| Module |
dimred |
| Description |
Usage |
| Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. |
  |
| output value |
type |
| the projections of the input coordinates on the PCA components that were found from the covariance matrix |
matrix |
Details and examples
Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input.
Principal component analysis is a statistical technique that uses an orthogonal transformation to convert a set of observations of
poorly correlated variables into a set of linearly uncorrelated variables. You can read more about the specifics of this technique
here
When used with molecular dynamics simulations a set of frames taken from the trajectory, , or the values of
a number of collective variables which are calculated from the trajectory frames are used as input. In this second instance your
input to the PCA analysis algorithm is thus a set of high-dimensional vectors of collective variables. However, if
collective variables are calculated from the positions of the atoms or if the positions are used directly the assumption is that
this input trajectory is a set of poorly correlated (high-dimensional) vectors. After principal component analysis has been
performed the output is a set of orthogonal vectors that describe the directions in which the largest motions have been seen.
In other words, principal component analysis provides a method for lowering the dimensionality of the data contained in a trajectory.
These output directions are some linear combination of the , and positions if the positions were used as input
or some linear combination of the input collective variables if a high-dimensional vector of collective variables was used as input.
As explained on the Wikipedia page you must calculate the average and covariance for each of the input coordinates. In other words, you must
calculate the average structure and the amount the system fluctuates around this average structure. The problem in doing so when the
, and coordinates of a molecule are used as input is that the majority of the changes in the positions of the
atoms comes from the translational and rotational degrees of freedom of the molecule. The first six principal components will thus, most likely,
be uninteresting. Consequently, to remedy this problem PLUMED provides the functionality to perform an RMSD alignment of the all the structures
to be analyzed to the first frame in the trajectory. This can be used to effectively remove translational and/or rotational motions from
consideration. The resulting principal components thus describe vibrational motions of the molecule.
If you wish to calculate the projection of a trajectory on a set of principal components calculated from this PCA action then the output can be
used as input for the PCAVARS action.
Examples
The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the positions
of the first 22 atoms. The TYPE=OPTIMAL instruction ensures that translational and rotational degrees of freedom are removed from consideration.
The average position and the first two principal components will be output to a file called pca-comp.pdb. Trajectory frames will be collected on every step and the PCA calculation
will be performed at the end of the simulation. The colvar file that is output contains the projections of all the positions in the high dimensional space on these vectors.
ffThe COLLECT_FRAMES action with label ff calculates the following quantities:| Quantity | Type | Description |
| ff_data | matrix | the data that is being collected by this action |
| ff_logweights | vector | the logarithms of the weights of the data points |
: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis This action is a shortcut and it has hidden defaults. More details ATOMSlist of atomic positions that you would like to collect and store for later analysis=1-22 STRIDE the frequency with which data should be stored for analysis=1
The COLLECT_FRAMES action with label ff calculates the following quantities:| Quantity | Description |
| ff.data | the data that is being collected by this action |
| ff.logweights | the logarithms of the weights of the data points |
ff: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis This action is a shortcut and uses the defaults shown here. More details ATOMSlist of atomic positions that you would like to collect and store for later analysis=1-22 STRIDE the frequency with which data should be stored for analysis=1 CLEAR the frequency with which data should all be deleted and restarted=0 ALIGN if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL=OPTIMAL
# ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1
ff_getposxThe POSITION action with label ff_getposx calculates the following quantities:| Quantity | Type | Description |
| ff_getposx.x | vector | the x-component of the atom position |
| ff_getposx.y | vector | the y-component of the atom position |
| ff_getposx.z | vector | the z-component of the atom position |
: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMSthe atom numbers that you would like to use the positions of=1-22
ff_getposThe CONCATENATE action with label ff_getpos calculates the following quantities:| Quantity | Type | Description |
| ff_getpos | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=ff_getposx.x,ff_getposx.y,ff_getposx.z
ff_cposxThe MEAN action with label ff_cposx calculates the following quantities:| Quantity | Type | Description |
| ff_cposx | scalar | the MEAN of the elements in the input value |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=ff_getposx.x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ff_cposyThe MEAN action with label ff_cposy calculates the following quantities:| Quantity | Type | Description |
| ff_cposy | scalar | the MEAN of the elements in the input value |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=ff_getposx.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ff_cposzThe MEAN action with label ff_cposz calculates the following quantities:| Quantity | Type | Description |
| ff_cposz | scalar | the MEAN of the elements in the input value |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe vector/matrix/grid whose elements shuld be added together=ff_getposx.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ff_refxThe CUSTOM action with label ff_refx calculates the following quantities:| Quantity | Type | Description |
| ff_refx | 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=ff_getposx.x,ff_cposx 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
ff_refyThe CUSTOM action with label ff_refy calculates the following quantities:| Quantity | Type | Description |
| ff_refy | 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=ff_getposx.y,ff_cposy 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
ff_refzThe CUSTOM action with label ff_refz calculates the following quantities:| Quantity | Type | Description |
| ff_refz | 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=ff_getposx.z,ff_cposz 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
ff_refThe CONCATENATE action with label ff_ref calculates the following quantities:| Quantity | Type | Description |
| ff_ref | vector | the concatenated vector/matrix that was constructed from the input values |
: CONCATENATEJoin vectors or matrices together More details ARGthe values that should be concatenated together to form the output vector=ff_refx,ff_refy,ff_refz
ff_refposThe COLLECT action with label ff_refpos calculates the following quantities:| Quantity | Type | Description |
| ff_refpos | matrix | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details TYPE required if you are collecting an object with rank>0=matrix ARGthe label of the value whose time series is being stored for later analysis=ff_ref STRIDE the frequency with which the data should be collected and added to the quantity being averaged=0 CLEAR the frequency with which to clear all the accumulated data=0
ff_refposTThe TRANSPOSE action with label ff_refposT calculates the following quantities:| Quantity | Type | Description |
| ff_refposT | vector | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ff_refpos
ff_rmsdThe RMSD action with label ff_rmsd calculates the following quantities:| Quantity | Type | Description |
| ff_rmsd.dist | scalar | the RMSD distance the atoms have moved |
| ff_rmsd.disp | vector | the vector of displacements for the atoms |
: RMSD_VECTOR More details ARGthe labels of two actions that you are calculating the RMSD between=ff_getpos,ff_refpos DISPLACEMENT Calculate the vector of displacements instead of the length of this vector SQUARED This should be set if you want mean squared displacement instead of RMSD TYPE the manner in which RMSD alignment is performed=OPTIMAL
ff_fposThe COMBINE action with label ff_fpos calculates the following quantities:| Quantity | Type | Description |
| ff_fpos | vector | the vector obtained by doing an element-wise application of a linear combination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ff_refposT,ff_rmsd.disp PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ff_dataThe COLLECT action with label ff_data calculates the following quantities:| Quantity | Type | Description |
| ff_data | matrix | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details TYPE required if you are collecting an object with rank>0=matrix ARGthe label of the value whose time series is being stored for later analysis=ff_fpos STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0
ff_cweightThe CONSTANT action with label ff_cweight calculates the following quantities:| Quantity | Type | Description |
| ff_cweight | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=0
ff_logweightsThe COLLECT action with label ff_logweights calculates the following quantities:| Quantity | Type | Description |
| ff_logweights | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=ff_cweight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0
ff_oneThe CONSTANT action with label ff_one calculates the following quantities:| Quantity | Type | Description |
| ff_one | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
ff_onesThe COLLECT action with label ff_ones calculates the following quantities:| Quantity | Type | Description |
| ff_ones | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=ff_one STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 CLEAR the frequency with which to clear all the accumulated data=0
# --- End of included input --- pcaThe PCA action with label pca calculates the following quantities:| Quantity | Type | Description |
| pca | matrix | the projections of the input coordinates on the PCA components that were found from the covariance matrix |
: PCAPerform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. This action is a shortcut and it has hidden defaults. More details ARGthe arguments that you would like to make the histogram for=ff NLOW_DIMnumber of low-dimensional coordinates required=2 FILEthe file on which to output the low dimensional coordinates=pca-comp.pdb
pca: PCAPerform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. This action is a shortcut and uses the defaults shown here. More details ARGthe arguments that you would like to make the histogram for=ff NLOW_DIMnumber of low-dimensional coordinates required=2 FILEthe file on which to output the low dimensional coordinates=pca-comp.pdb STRIDE the frequency with which to perform this analysis=0
# pca: PCA ARG=ff NLOW_DIM=2 FILE=pca-comp.pdb
pca_weightsThe CUSTOM action with label pca_weights calculates the following quantities:| Quantity | Type | Description |
| pca_weights | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: LOGSUMEXPThis action takes the exponential of a vector of logarithms and divides each element of the vector by the sum of the exponentials. More details ARGthe vector of logweights that you would like to normalise using the logsumexp trick=ff_logweights
pca_dataTThe TRANSPOSE action with label pca_dataT calculates the following quantities:| Quantity | Type | Description |
| pca_dataT | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ff_data
pca_meanThe MATRIX_VECTOR_PRODUCT action with label pca_mean calculates the following quantities:| Quantity | Type | Description |
| pca_mean | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=pca_dataT,pca_weights
pca_averagesThe OUTER_PRODUCT action with label pca_averages calculates the following quantities:| Quantity | Type | Description |
| pca_averages | matrix | a matrix containing the outer product of the two input vectors that was obtained using the function that was input |
: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=ff_ones,pca_mean
pca_wonesThe CONSTANT action with label pca_wones calculates the following quantities:| Quantity | Type | Description |
| pca_wones | 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=1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
pca_wmatThe OUTER_PRODUCT action with label pca_wmat calculates the following quantities:| Quantity | Type | Description |
| pca_wmat | matrix | a matrix containing the outer product of the two input vectors that was obtained using the function that was input |
: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=pca_weights,pca_wones
pca_diffThe CUSTOM action with label pca_diff calculates the following quantities:| Quantity | Type | Description |
| pca_diff | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ff_data,pca_averages 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
pca_wdiffThe CUSTOM action with label pca_wdiff calculates the following quantities:| Quantity | Type | Description |
| pca_wdiff | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=pca_wmat,pca_diff FUNCthe function you wish to evaluate=sqrt(x)*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
pca_wdiffTThe TRANSPOSE action with label pca_wdiffT calculates the following quantities:| Quantity | Type | Description |
| pca_wdiffT | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=pca_wdiff
pca_covarThe MATRIX_PRODUCT action with label pca_covar calculates the following quantities:| Quantity | Type | Description |
| pca_covar | matrix | the product of the two input matrices |
: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=pca_wdiffT,pca_wdiff
pca_eigThe DIAGONALIZE action with label pca_eig calculates the following quantities:| Quantity | Type | Description |
| pca_eig.vals-1 | scalar | the eigevalues of the input matrix This is the 1th of these quantities |
| pca_eig.vecs-1 | vector | the eigenvectors of the input matrix This is the 1th of these quantities |
| pca_eig.vals-2 | scalar | the eigevalues of the input matrix This is the 2th of these quantities |
| pca_eig.vecs-2 | vector | the eigenvectors of the input matrix This is the 2th of these quantities |
: DIAGONALIZECalculate the eigenvalues and eigenvectors of a square matrix More details ARGthe input matrix=pca_covar VECTORS the eigenvalues and vectors that you would like to calculate=1,2
pca_pcaTThe VSTACK action with label pca_pcaT calculates the following quantities:| Quantity | Type | Description |
| pca_pcaT | matrix | a matrix that contains the input vectors in its columns |
: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=pca_mean,pca_eig.vecs-1,pca_eig.vecs-2
pca_pcaThe TRANSPOSE action with label pca_pca calculates the following quantities:| Quantity | Type | Description |
| pca_pca | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=pca_pcaT
DUMPPDBOutput PDB file. More details DESCRIPTIONthe title to use for your PDB output=PCA ATOM_INDICESthe indices of the atoms in your PDB output=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 ATOMSvalue containing positions of atoms that should be output=pca_pca FILEthe name of the file on which to output these quantities=pca-comp.pdb STRIDE the frequency with which the atoms should be output=0
The DUMPPDB action with label calculates somethingpca_eigvThe VSTACK action with label pca_eigv calculates the following quantities:| Quantity | Type | Description |
| pca_eigv | matrix | a matrix that contains the input vectors in its columns |
: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=pca_eig.vecs-1,pca_eig.vecs-2
pcaThe MATRIX_PRODUCT action with label pca calculates the following quantities:| Quantity | Type | Description |
| pca | matrix | the product of the two input matrices |
: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=pca_diff,pca_eigv
# --- End of included input --- DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=pca,pca_weights FILE the file on which to write the vetors=colvar STRIDE the frequency with which the grid should be output to the file=0
The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the six distances
seen in the input file below. In this calculation the first two principal components will be output to a file called PCA-comp.pdb.
Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps. Consequently, if you run a 2000 step simulation the
PCA analysis will be performed twice. The REWEIGHT_BIAS action in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
when calculating averages and covariance matrices a reweighting should be performed based and each frames' weight in these calculations should be determined based on
the current value of the instantaneous bias (see REWEIGHT_BIAS).
d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities:| Quantity | Type | Description |
| d2 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,3
d3The DISTANCE action with label d3 calculates the following quantities:| Quantity | Type | Description |
| d3 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4
d4The DISTANCE action with label d4 calculates the following quantities:| Quantity | Type | Description |
| d4 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,3
d5The DISTANCE action with label d5 calculates the following quantities:| Quantity | Type | Description |
| d5 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4
d6The DISTANCE action with label d6 calculates the following quantities:| Quantity | Type | Description |
| d6 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
rrThe RESTRAINT action with label rr calculates the following quantities:| Quantity | Type | Description |
| rr.bias | scalar | the instantaneous value of the bias potential |
| rr.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action has hidden defaults. More details ARGthe values the harmonic restraint acts upon=d1 ATthe position of the restraint=0.1 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10
rr: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. This action uses the defaults shown here. More details ARGthe values the harmonic restraint acts upon=d1 ATthe position of the restraint=0.1 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10 SLOPE specifies that the restraint is linear and what the values of the force constants on each of the variables are=0.0
rbiasThe REWEIGHT_BIAS action with label rbias calculates the following quantities:| Quantity | Type | Description |
| rbias | scalar | the weight to use for this frame to negate the effect the bias |
: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action has hidden defaults. More details TEMPthe system temperature=300
rbias: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored This action uses the defaults shown here. More details TEMPthe system temperature=300 ARG the biases that must be taken into account when reweighting=*.bias
ffThe COLLECT_FRAMES action with label ff calculates the following quantities:| Quantity | Type | Description |
| ff_data | matrix | the data that is being collected by this action |
| ff_logweights | vector | the logarithms of the weights of the data points |
: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis This action is a shortcut and it has hidden defaults. More details ARGthe labels of the values whose time series you would like to collect for later analysis=d1,d2,d3,d4,d5,d6 LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations when calculating averages=rbias STRIDE the frequency with which data should be stored for analysis=5
The COLLECT_FRAMES action with label ff calculates the following quantities:| Quantity | Description |
| ff.data | the data that is being collected by this action |
| ff.logweights | the logarithms of the weights of the data points |
ff: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis This action is a shortcut and uses the defaults shown here. More details ARGthe labels of the values whose time series you would like to collect for later analysis=d1,d2,d3,d4,d5,d6 LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations when calculating averages=rbias STRIDE the frequency with which data should be stored for analysis=5 CLEAR the frequency with which data should all be deleted and restarted=0
# ff: COLLECT_FRAMES ARG=d1,d2,d3,d4,d5,d6 LOGWEIGHTS=rbias STRIDE=5
ff_d1The COLLECT action with label ff_d1 calculates the following quantities:| Quantity | Type | Description |
| ff_d1 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_d2The COLLECT action with label ff_d2 calculates the following quantities:| Quantity | Type | Description |
| ff_d2 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_d3The COLLECT action with label ff_d3 calculates the following quantities:| Quantity | Type | Description |
| ff_d3 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d3 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_d4The COLLECT action with label ff_d4 calculates the following quantities:| Quantity | Type | Description |
| ff_d4 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d4 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_d5The COLLECT action with label ff_d5 calculates the following quantities:| Quantity | Type | Description |
| ff_d5 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d5 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_d6The COLLECT action with label ff_d6 calculates the following quantities:| Quantity | Type | Description |
| ff_d6 | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=d6 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_dataThe VSTACK action with label ff_data calculates the following quantities:| Quantity | Type | Description |
| ff_data | matrix | a matrix that contains the input vectors in its columns |
: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=ff_d1,ff_d2,ff_d3,ff_d4,ff_d5,ff_d6
ff_logweightsThe COLLECT action with label ff_logweights calculates the following quantities:| Quantity | Type | Description |
| ff_logweights | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=rbias STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
ff_oneThe CONSTANT action with label ff_one calculates the following quantities:| Quantity | Type | Description |
| ff_one | scalar | the constant value that was read from the plumed input |
: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
ff_onesThe COLLECT action with label ff_ones calculates the following quantities:| Quantity | Type | Description |
| ff_ones | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis More details ARGthe label of the value whose time series is being stored for later analysis=ff_one STRIDE the frequency with which the data should be collected and added to the quantity being averaged=5 CLEAR the frequency with which to clear all the accumulated data=0
# --- End of included input --- pcaThe PCA action with label pca calculates the following quantities:| Quantity | Type | Description |
| pca | matrix | the projections of the input coordinates on the PCA components that were found from the covariance matrix |
: PCAPerform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. This action is a shortcut and it has hidden defaults. More details ARGthe arguments that you would like to make the histogram for=ff NLOW_DIMnumber of low-dimensional coordinates required=2 FILEthe file on which to output the low dimensional coordinates=pca-comp.pdb
pca: PCAPerform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input. This action is a shortcut and uses the defaults shown here. More details ARGthe arguments that you would like to make the histogram for=ff NLOW_DIMnumber of low-dimensional coordinates required=2 FILEthe file on which to output the low dimensional coordinates=pca-comp.pdb STRIDE the frequency with which to perform this analysis=0 FMT the format to use when outputting the low dimensional coordinates=%f
# pca: PCA ARG=ff NLOW_DIM=2 FILE=pca-comp.pdb
pca_weightsThe CUSTOM action with label pca_weights calculates the following quantities:| Quantity | Type | Description |
| pca_weights | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: LOGSUMEXPThis action takes the exponential of a vector of logarithms and divides each element of the vector by the sum of the exponentials. More details ARGthe vector of logweights that you would like to normalise using the logsumexp trick=ff_logweights
pca_dataTThe TRANSPOSE action with label pca_dataT calculates the following quantities:| Quantity | Type | Description |
| pca_dataT | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=ff_data
pca_meanThe MATRIX_VECTOR_PRODUCT action with label pca_mean calculates the following quantities:| Quantity | Type | Description |
| pca_mean | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=pca_dataT,pca_weights
pca_averagesThe OUTER_PRODUCT action with label pca_averages calculates the following quantities:| Quantity | Type | Description |
| pca_averages | matrix | a matrix containing the outer product of the two input vectors that was obtained using the function that was input |
: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=ff_ones,pca_mean
pca_wonesThe CONSTANT action with label pca_wones calculates the following quantities:| Quantity | Type | Description |
| pca_wones | 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=1,1,1,1,1,1
pca_wmatThe OUTER_PRODUCT action with label pca_wmat calculates the following quantities:| Quantity | Type | Description |
| pca_wmat | matrix | a matrix containing the outer product of the two input vectors that was obtained using the function that was input |
: OUTER_PRODUCTCalculate the outer product matrix of two vectors More details ARGthe labels of the two vectors from which the outer product is being computed=pca_weights,pca_wones
pca_diffThe CUSTOM action with label pca_diff calculates the following quantities:| Quantity | Type | Description |
| pca_diff | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=ff_data,pca_averages 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
pca_wdiffThe CUSTOM action with label pca_wdiff calculates the following quantities:| Quantity | Type | Description |
| pca_wdiff | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=pca_wmat,pca_diff FUNCthe function you wish to evaluate=sqrt(x)*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
pca_wdiffTThe TRANSPOSE action with label pca_wdiffT calculates the following quantities:| Quantity | Type | Description |
| pca_wdiffT | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=pca_wdiff
pca_covarThe MATRIX_PRODUCT action with label pca_covar calculates the following quantities:| Quantity | Type | Description |
| pca_covar | matrix | the product of the two input matrices |
: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=pca_wdiffT,pca_wdiff
pca_eigThe DIAGONALIZE action with label pca_eig calculates the following quantities:| Quantity | Type | Description |
| pca_eig.vals-1 | scalar | the eigevalues of the input matrix This is the 1th of these quantities |
| pca_eig.vecs-1 | vector | the eigenvectors of the input matrix This is the 1th of these quantities |
| pca_eig.vals-2 | scalar | the eigevalues of the input matrix This is the 2th of these quantities |
| pca_eig.vecs-2 | vector | the eigenvectors of the input matrix This is the 2th of these quantities |
: DIAGONALIZECalculate the eigenvalues and eigenvectors of a square matrix More details ARGthe input matrix=pca_covar VECTORS the eigenvalues and vectors that you would like to calculate=1,2
pca_pcaTThe VSTACK action with label pca_pcaT calculates the following quantities:| Quantity | Type | Description |
| pca_pcaT | matrix | a matrix that contains the input vectors in its columns |
: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=pca_mean,pca_eig.vecs-1,pca_eig.vecs-2
pca_pcaThe TRANSPOSE action with label pca_pca calculates the following quantities:| Quantity | Type | Description |
| pca_pca | matrix | the transpose of the input matrix |
: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=pca_pcaT
DUMPPDBOutput PDB file. More details DESCRIPTIONthe title to use for your PDB output=PCA ARG_NAMESthe names of the arguments that are being output=d1,d2,d3,d4,d5,d6 ARGthe values that are being output in the PDB file=pca_pca FILEthe name of the file on which to output these quantities=pca-comp.pdb STRIDE the frequency with which the atoms should be output=0 FMTthe format that should be used to output real numbers in the title=%f
The DUMPPDB action with label calculates somethingpca_eigvThe VSTACK action with label pca_eigv calculates the following quantities:| Quantity | Type | Description |
| pca_eigv | matrix | a matrix that contains the input vectors in its columns |
: VSTACKCreate a matrix by stacking vectors together More details ARGthe values that you would like to stack together to construct the output matrix=pca_eig.vecs-1,pca_eig.vecs-2
pcaThe MATRIX_PRODUCT action with label pca calculates the following quantities:| Quantity | Type | Description |
| pca | matrix | the product of the two input matrices |
: MATRIX_PRODUCTCalculate the product of two matrices More details ARGthe label of the two matrices from which the product is calculated=pca_diff,pca_eigv
# --- End of included input --- DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=pca,pca_weights FILE the file on which to write the vetors=colvar STRIDE the frequency with which the grid should be output to the file=1000
Full list of keywords
The following table describes the keywords and options that can be used with this action
| Keyword |
Type |
Default |
Description |
| ARG |
compulsory |
none |
the arguments that you would like to make the histogram for |
| NLOW_DIM |
compulsory |
none |
number of low-dimensional coordinates required |
| STRIDE |
compulsory |
0 |
the frequency with which to perform this analysis |
| FMT |
compulsory |
%f |
the format to use when outputting the low dimensional coordinates |
| FILE |
optional |
not used |
the file on which to output the low dimensional coordinates |
