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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 ouput 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.
| 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 |
| PRECISION | The number of digits in trajectory file |
| TYPE | file type, either xyz, gro, xtc, or trr, can override an automatically detected file extension |
| 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 |
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.
COM ATOMS=11-20 LABEL=c1 DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1
(see also COM)
The following input is very similar but dumps a .gro (gromacs) file, which also contains atom and residue names.
# this is required to have proper atom names: MOLINFO STRUCTURE=reference.pdb # if omitted, atoms will have "X" name... COM ATOMS=11-20 LABEL=c1 DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1 # notice that last atom is a virtual one and will not have # a correct name in the resulting gro file
1.8.10 
