| Module |
generic |
| Description |
Usage |
| Output PDB file. |
  |
| This action outputs data to a file. You can read more about how PLUMED manages output files here |
|
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 |
vector/matrix |
the values that are being output in the PDB file |
Further details and examples
Output PDB file.
This command can be used to output a PDB file that contains the result from a dimensionality reduction
calculation. To understand how to use this command you are best off looking at the examples of dimensionality
reduction calculations that are explained in the documentation of the actions in the dimred module.
Please note that this command cannot be used in place of DUMPATOMS to output a pdb file rather than
a gro or xyz file. This is an example where this command is used to output atomic positions:
Click on the labels of the actions for more information on what each action computes
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 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=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 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=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 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=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_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=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 compbination 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 --- DUMPPDBOutput PDB file. More details ATOM_INDICESthe indices of the atoms in your PDB output=1-22 ATOMSvalue containing positions of atoms that should be output=ff_data FILEthe name of the file on which to output these quantities=pos.pdb
From this example alone it is clear that this command works very differently to the DUMPATOMS command.
Notice, furthermore, that you can output the positions of atoms along with the argument values that correspond to each
set of atomic positions as follows:
Click on the labels of the actions for more information on what each action computes
dThe DISTANCE action with label d calculates the following quantities:| Quantity | Type | Description |
| d | 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
cdThe COLLECT action with label cd calculates the following quantities:| Quantity | Type | Description |
| cd | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=d
cd: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=d STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
aThe ANGLE action with label a calculates the following quantities:| Quantity | Type | Description |
| a | scalar | the ANGLE involving these atoms |
: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=1,2,3
caThe COLLECT action with label ca calculates the following quantities:| Quantity | Type | Description |
| ca | vector | the time series for the input quantity |
: COLLECTCollect data from the trajectory for later analysis This action has hidden defaults. More details ARGthe label of the value whose time series is being stored for later analysis=a
ca: COLLECTCollect data from the trajectory for later analysis This action uses the defaults shown here. More details ARGthe label of the value whose time series is being stored for later analysis=a STRIDE the frequency with which the data should be collected and added to the quantity being averaged=1 TYPE required if you are collecting an object with rank>0=auto CLEAR the frequency with which to clear all the accumulated data=0
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 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=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 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=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 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=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_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=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 compbination 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 ---
DUMPPDBOutput PDB file. More details ATOM_INDICESthe indices of the atoms in your PDB output=1-22 ATOMSvalue containing positions of atoms that should be output=ff_data ARGthe values that are being output in the PDB file=cd,ca FILEthe name of the file on which to output these quantities=pos.pdb
The outputted pdb file has the format described in the documentation for the PDB2CONSTANT action.
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword |
Type |
Default |
Description |
| ARG |
input |
none |
the values that are being output in the PDB file |
| STRIDE |
compulsory |
0 |
the frequency with which the atoms should be output |
| FILE |
compulsory |
none |
the name of the file on which to output these quantities |
| FMT |
compulsory |
%f |
the format that should be used to output real numbers |
| OCCUPANCY |
compulsory |
1.0 |
vector of values to output in the occupancy column of the pdb file |
| BETA |
compulsory |
1.0 |
vector of values to output in the beta column of the pdb file |
| ATOMS |
optional |
not used |
value containing positions of atoms that should be output |
| DESCRIPTION |
optional |
not used |
the title to use for your PDB output |
| ATOM_INDICES |
optional |
not used |
the indices of the atoms in your PDB output |
| RESIDUE_INDICES |
optional |
not used |
the indices of the residues in your PDB output |
| ARG_NAMES |
optional |
not used |
the names of the arguments that are being output |
