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| This is part of the generic module |
Dump selected atoms on a file.
This command can be used to output the positions of a particular set of atoms. The atoms required are output in a xyz or gro formatted file. If PLUMED has been compiled with xdrfile support, then also xtc and trr files can be written. To this aim one should install xdrfile library (http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library). If the xdrfile library is installed properly the PLUMED configure script should be able to detect it and enable it. The type of file is automatically detected from the file extension, but can be also enforced with TYPE. Importantly, if your input file contains actions that edit the atoms position (e.g. WHOLEMOLECULES) and the DUMPATOMS command appears after this instruction, then the edited atom positions are output. You can control the buffering of output using the FLUSH keyword on a separate line.
Units of the printed file can be controlled with the UNITS keyword. By default PLUMED units as controlled in the UNITS command are used, but one can override it e.g. with UNITS=A. Notice that gro/xtc/trr files can only contain coordinates in nm.
The following input instructs plumed to print out the positions of atoms 1-10 together with the position of the center of mass of atoms 11-20 every 10 steps to a file called file.xyz.
c1: COMATOMS=11-20 DUMPATOMSthe list of atoms which are involved the virtual atom's definition.STRIDE=10compulsory keyword ( default=1 ) the frequency with which the atoms should be outputFILE=file.xyzcompulsory keyword file on which to output coordinates; extension is automatically detectedATOMS=1-10,c1the atom indices whose positions you would like to print out.
Notice that the coordinates in the xyz file will be expressed in nm, since these are the defaults units in PLUMED. If you want the xyz file to be expressed in A, you should use the following input
c1: COMATOMS=11-20 DUMPATOMSthe list of atoms which are involved the virtual atom's definition.STRIDE=10compulsory keyword ( default=1 ) the frequency with which the atoms should be outputFILE=file.xyzcompulsory keyword file on which to output coordinates; extension is automatically detectedATOMS=1-10,c1the atom indices whose positions you would like to print out.UNITS=Acompulsory keyword ( default=PLUMED ) the units in which to print out the coordinates.
As an alternative, you might want to set all the length used by PLUMED to Angstrom using the UNITS action. However, this latter choice will affect all your input and output.
The following input is very similar but dumps a .gro (gromacs) file, which also contains atom and residue names.
#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb # this is required to have proper atom names: MOLINFOSTRUCTURE=reference.pdb # if omitted, atoms will have "X" name... c1: COMcompulsory keyword a file in pdb format containing a reference structure.ATOMS=11-20 DUMPATOMSthe list of atoms which are involved the virtual atom's definition.STRIDE=10compulsory keyword ( default=1 ) the frequency with which the atoms should be outputFILE=file.grocompulsory keyword file on which to output coordinates; extension is automatically detectedATOMS=1-10,c1 # notice that last atom is a virtual one and will not have # a correct name in the resulting gro filethe atom indices whose positions you would like to print out.
The file.gro will contain coordinates expressed in nm, since this is the convention for gro files.
In case you have compiled PLUMED with xdrfile library, you might even write xtc or trr files as follows
c1: COMATOMS=11-20 DUMPATOMSthe list of atoms which are involved the virtual atom's definition.STRIDE=10compulsory keyword ( default=1 ) the frequency with which the atoms should be outputFILE=file.xtccompulsory keyword file on which to output coordinates; extension is automatically detectedATOMS=1-10,c1the atom indices whose positions you would like to print out.
Notice that xtc files are significantly smaller than gro and xyz files.
Finally, consider that gro and xtc file store coordinates with limited precision set by the PRECISION keyword. Default value is 3, which means "3 digits after dot" in nm (1/1000 of a nm). The following will write a larger xtc file with high resolution coordinates:
c1: COMATOMS=11-20 DUMPATOMSthe list of atoms which are involved the virtual atom's definition.STRIDE=10compulsory keyword ( default=1 ) the frequency with which the atoms should be outputFILE=file.xtccompulsory keyword file on which to output coordinates; extension is automatically detectedATOMS=1-10,c1the atom indices whose positions you would like to print out.PRECISION=7The number of digits in trajectory file
| ATOMS | the atom indices whose positions you would like to print out. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
| STRIDE | ( default=1 ) the frequency with which the atoms should be output |
| FILE | file on which to output coordinates; extension is automatically detected |
| UNITS | ( default=PLUMED ) the units in which to print out the coordinates. PLUMED means internal PLUMED units |
| ARG | the labels of vectors that should be output in the xyz file. The number of elements in the vector should equal the number of atoms output |
| PRECISION | The number of digits in trajectory file |
| TYPE | file type, either xyz, gro, xtc, or trr, can override an automatically detected file extension |
| LESS_THAN_OR_EQUAL | when printing with arguments that are vectors only print components of vectors have a value less than or equal to this value |
| GREATER_THAN_OR_EQUAL | when printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value |
| RESTART | allows per-action setting of restart (YES/NO/AUTO) |
| UPDATE_FROM | Only update this action from this time |
| UPDATE_UNTIL | Only update this action until this time |
1.8.17