Action: DUMPPDB
| 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 |
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:
ff: 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 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.
As indcated below, you can specify what should appear in the title line of your PDB file as well as the residue indices, occupancies and beta values for each of the collected atoms.
ff: 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=1-4 STRIDE the frequency with which data should be stored for analysis=1 CLEAR the frequency with which data should all be deleted and restarted=100 DUMPPDBOutput PDB file. More details ... ATOM_INDICESthe indices of the atoms in your PDB output=1-4 ATOMSvalue containing positions of atoms that should be output=ff_data DESCRIPTIONthe title to use for your PDB output=title RESIDUE_INDICESthe indices of the residues in your PDB output=1,1,2,2 OCCUPANCY vector of values to output in the occupancy column of the pdb file=1,0.5,0.5,0.75 BETA vector of values to output in the beta column of the pdb file=0.5,1,0.2,0.6 FILEthe name of the file on which to output these quantities=pos.pdb STRIDE the frequency with which the atoms should be output=100 ...
Notice, furthermore, that we store 100 and output 100 frame blocks of data here from the trajectory. The input above will thus output multiple pdb files.
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:
# Calculate the distance between atoms 1 and 2 d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 # Collect the distance between atoms 1 and 2 cd: 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 # Calculate the angle involving atoms 1, 2 and 3 a: 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 # Collect the angle involving atoms 1, 2 and 3 ca: 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 # Now collect the positions ff: 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 # Output a PDB file that contains the collected atomic positions # and the collected distances and angles 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.
The names that are used for each of the arguments in the pdb file are the same as the labels of the values in the input above (d and a in the above case).
If for any reason you want to use different names for each of the arguments in the PDB file you can use the ARG_NAMES keyword as
shown below:
# Calculate the distance between atoms 1 and 2 d: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 # Collect the distance between atoms 1 and 2 cd: 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 # Calculate the angle involving atoms 1, 2 and 3 a: 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 # Collect the angle involving atoms 1, 2 and 3 ca: 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 # Now collect the positions ff: 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 # Output a PDB file that contains the collected atomic positions # and the collected distances and angles 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 ARG_NAMESthe names of the arguments that are being output=m,n FILEthe name of the file on which to output these quantities=pos.pdb
The distance will be shown with the name m for the input above while the angle will have the name n.
Input
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 |
Full list of keywords
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 |
| 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 |