| Module |
landmarks |
| Description |
Usage |
| Collect atomic positions or argument values from the trajectory for later analysis |
  |
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 |
| data |
matrix |
the data that is being collected by this action |
| logweights |
vector |
the logarithms of the weights of the data points |
The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword |
Type |
Description |
| ARG |
scalar/vector |
the labels of the values whose time series you would like to collect for later analysis |
Further details and examples
Collect atomic positions or argument values from the trajectory for later analysis
This shortcut uses COLLECT actions to collect data from the trajectory that is amenable for later analysis
using PLUMED's landmark selection actions or dimensionality reduction methods. You can use this method to collect atomic position
data as shown in the following example:
Click on the labels of the actions for more information on what each action computes
ccThe COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Type | Description |
| cc_data | matrix | the data that is being collected by this action |
| cc_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=1,2,3,4,5,6,7,8,9,10 ALIGN if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL=OPTIMAL
The COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Description |
| cc.data | the data that is being collected by this action |
| cc.logweights | the logarithms of the weights of the data points |
cc: 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=1,2,3,4,5,6,7,8,9,10 ALIGN if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL=OPTIMAL 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
# cc: COLLECT_FRAMES ATOMS=1,2,3,4,5,6,7,8,9,10 ALIGN=OPTIMAL
cc_getposxThe POSITION action with label cc_getposx calculates the following quantities:| Quantity | Type | Description |
| cc_getposx.x | vector | the x-component of the atom position |
| cc_getposx.y | vector | the y-component of the atom position |
| cc_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=1,2,3,4,5,6,7,8,9,10
cc_getposThe CONCATENATE action with label cc_getpos calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_getposx.x,cc_getposx.y,cc_getposx.z
cc_cposxThe MEAN action with label cc_cposx calculates the following quantities:| Quantity | Type | Description |
| cc_cposx | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cc_getposx.x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cc_cposyThe MEAN action with label cc_cposy calculates the following quantities:| Quantity | Type | Description |
| cc_cposy | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cc_getposx.y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cc_cposzThe MEAN action with label cc_cposz calculates the following quantities:| Quantity | Type | Description |
| cc_cposz | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=cc_getposx.z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cc_refxThe CUSTOM action with label cc_refx calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_getposx.x,cc_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
cc_refyThe CUSTOM action with label cc_refy calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_getposx.y,cc_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
cc_refzThe CUSTOM action with label cc_refz calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_getposx.z,cc_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
cc_refThe CONCATENATE action with label cc_ref calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_refx,cc_refy,cc_refz
cc_refposThe COLLECT action with label cc_refpos calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_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
cc_refposTThe TRANSPOSE action with label cc_refposT calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_refpos
cc_rmsdThe RMSD action with label cc_rmsd calculates the following quantities:| Quantity | Type | Description |
| cc_rmsd.dist | scalar | the RMSD distance the atoms have moved |
| cc_rmsd.disp | vector | the vector of displacements for the atoms |
: RMSD_VECTORCalculate the RMSD distance between the instaneous configuration and multiple reference configurations More details ARGthe labels of two actions that you are calculating the RMSD between=cc_getpos,cc_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
cc_fposThe COMBINE action with label cc_fpos calculates the following quantities:| Quantity | Type | Description |
| cc_fpos | vector | the vector obtained by doing an element-wise application of a linear compbination to the input vectors |
: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cc_refposT,cc_rmsd.disp PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cc_dataThe COLLECT action with label cc_data calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_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
cc_cweightThe CONSTANT action with label cc_cweight calculates the following quantities:| Quantity | Type | Description |
| cc_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
cc_logweightsThe COLLECT action with label cc_logweights calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_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
cc_oneThe CONSTANT action with label cc_one calculates the following quantities:| Quantity | Type | Description |
| cc_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
cc_onesThe COLLECT action with label cc_ones calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_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 ---
DUMPPDBOutput PDB file. More details ATOMSvalue containing positions of atoms that should be output=cc_data ATOM_INDICESthe indices of the atoms in your PDB output=1,2,3,4,5,6,7,8,9,10 FILEthe name of the file on which to output these quantities=traj.pdb
If you look at the expanded version of the shortcut above you can see how the position data is stored in a matrix. It is also worth
noting that all the stored structured are aligned to the first frame before being stored. When we take the difference between the
stored configurations we are thus excluding any rotation or the reference frame or translation of the center of mass that has taken place.
Instead of storing the positions of the atoms you you can store a time series of argument values as shown below:
Click on the labels of the actions for more information on what each action computes
t1The TORSION action with label t1 calculates the following quantities:| Quantity | Type | Description |
| t1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
t2The TORSION action with label t2 calculates the following quantities:| Quantity | Type | Description |
| t2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,6,7,8
t3The TORSION action with label t3 calculates the following quantities:| Quantity | Type | Description |
| t3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=9,10,11,12
ccThe COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Type | Description |
| cc_data | matrix | the data that is being collected by this action |
| cc_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. More details ARGthe labels of the values whose time series you would like to collect for later analysis=t1,t2,t3 STRIDE the frequency with which data should be stored for analysis=10 CLEAR the frequency with which data should all be deleted and restarted=1000
# cc: COLLECT_FRAMES ARG=t1,t2,t3 STRIDE=10 CLEAR=1000
The COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Description |
| cc.data | the data that is being collected by this action |
| cc.logweights | the logarithms of the weights of the data points |
cc_t1The COLLECT action with label cc_t1 calculates the following quantities:| Quantity | Type | Description |
| cc_t1 | 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=t1 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=10 CLEAR the frequency with which to clear all the accumulated data=1000
cc_t2The COLLECT action with label cc_t2 calculates the following quantities:| Quantity | Type | Description |
| cc_t2 | 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=t2 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=10 CLEAR the frequency with which to clear all the accumulated data=1000
cc_t3The COLLECT action with label cc_t3 calculates the following quantities:| Quantity | Type | Description |
| cc_t3 | 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=t3 STRIDE the frequency with which the data should be collected and added to the quantity being averaged=10 CLEAR the frequency with which to clear all the accumulated data=1000
cc_dataThe VSTACK action with label cc_data calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_t1,cc_t2,cc_t3
cc_cweightThe CONSTANT action with label cc_cweight calculates the following quantities:| Quantity | Type | Description |
| cc_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
cc_logweightsThe COLLECT action with label cc_logweights calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_cweight STRIDE the frequency with which the data should be collected and added to the quantity being averaged=10 CLEAR the frequency with which to clear all the accumulated data=1000
cc_oneThe CONSTANT action with label cc_one calculates the following quantities:| Quantity | Type | Description |
| cc_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
cc_onesThe COLLECT action with label cc_ones calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_one STRIDE the frequency with which the data should be collected and added to the quantity being averaged=10 CLEAR the frequency with which to clear all the accumulated data=1000
# --- End of included input --- DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=cc.* FILE the file on which to write the vetors=timeseries STRIDE the frequency with which the grid should be output to the file=1000
Notice that the stored data is in a matrix once again here. Further note that we are storing the three torsions on every tenth step. In addition we also delete all the stored data on every 1000th step of trajectory.
The time series for each consecutive 1000 step segment of trajectory will be output to separate files in the above input. These output files also contain weights for each of the stored frames. For the above input
these weights are all equal to one. We can, however, pass the weight as an input argument. This functionality is useful if a bias is acting upon the system and we want to keep track of how much bias is acting upon
each frame of the traejctory as has been done in the input below.
Click on the labels of the actions for more information on what each action computes
t1The TORSION action with label t1 calculates the following quantities:| Quantity | Type | Description |
| t1 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1,2,3,4
t2The TORSION action with label t2 calculates the following quantities:| Quantity | Type | Description |
| t2 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,6,7,8
t3The TORSION action with label t3 calculates the following quantities:| Quantity | Type | Description |
| t3 | scalar | the TORSION involving these atoms |
: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=9,10,11,12
rThe RESTRAINT action with label r calculates the following quantities:| Quantity | Type | Description |
| r.bias | scalar | the instantaneous value of the bias potential |
| r.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=t1 ATthe position of the restraint=pi/2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10
r: 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=t1 ATthe position of the restraint=pi/2 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
bwThe REWEIGHT_BIAS action with label bw calculates the following quantities:| Quantity | Type | Description |
| bw | 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
bw: 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
ccThe COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Type | Description |
| cc_data | matrix | the data that is being collected by this action |
| cc_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=t1,t2,t3 LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations when calculating averages=bw
The COLLECT_FRAMES action with label cc calculates the following quantities:| Quantity | Description |
| cc.data | the data that is being collected by this action |
| cc.logweights | the logarithms of the weights of the data points |
cc: 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=t1,t2,t3 LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations when calculating averages=bw 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
# cc: COLLECT_FRAMES ARG=t1,t2,t3 LOGWEIGHTS=bw
cc_t1The COLLECT action with label cc_t1 calculates the following quantities:| Quantity | Type | Description |
| cc_t1 | 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=t1 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
cc_t2The COLLECT action with label cc_t2 calculates the following quantities:| Quantity | Type | Description |
| cc_t2 | 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=t2 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
cc_t3The COLLECT action with label cc_t3 calculates the following quantities:| Quantity | Type | Description |
| cc_t3 | 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=t3 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
cc_dataThe VSTACK action with label cc_data calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_t1,cc_t2,cc_t3
cc_logweightsThe COLLECT action with label cc_logweights calculates the following quantities:| Quantity | Type | Description |
| cc_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=bw 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
cc_oneThe CONSTANT action with label cc_one calculates the following quantities:| Quantity | Type | Description |
| cc_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
cc_onesThe COLLECT action with label cc_ones calculates the following quantities:| Quantity | Type | Description |
| cc_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=cc_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 --- DUMPVECTORPrint a vector to a file More details ARGthe labels of vectors/matrices that should be output in the file=cc.* FILE the file on which to write the vetors=timeseries
You can learn how to use COLLECT_FRAMES to perform dimensionality reduction calculations by working through this tutorial
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword |
Type |
Default |
Description |
| ARG |
input |
none |
the labels of the values whose time series you would like to collect for later analysis |
| STRIDE |
compulsory |
1 |
the frequency with which data should be stored for analysis |
| CLEAR |
compulsory |
0 |
the frequency with which data should all be deleted and restarted |
| ALIGN |
compulsory |
OPTIMAL |
if storing atoms how would you like the alignment to be done can be SIMPLE/OPTIMAL |
| ATOMS |
optional |
not used |
list of atomic positions that you would like to collect and store for later analysis |
| LOGWEIGHTS |
optional |
not used |
list of actions that calculates log weights that should be used to weight configurations when calculating averages |
