DUMPATOMS

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.

Examples

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.

Click on the labels of the actions for more information on what each action computes

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c1 calculates the position of a virtual atom
DUMPATOMS 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=file.xyz 
ATOMS
the atom indices whose positions you would like to print out. 
=1-10,c1 The DUMPATOMS action with label 

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

Click on the labels of the actions for more information on what each action computes

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c1 calculates the position of a virtual atom
DUMPATOMS 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=file.xyz 
ATOMS
the atom indices whose positions you would like to print out. 
=1-10,c1 
UNITS
compulsory keyword ( default=PLUMED )
the units in which to print out the coordinates. 
=A The DUMPATOMS action with label 

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.

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
# this is required to have proper atom names:
MOLINFO 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=reference.pdb The MOLINFO action with label 
# if omitted, atoms will have "X" name...
c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c1 calculates the position of a virtual atom
DUMPATOMS 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=file.gro 
ATOMS
the atom indices whose positions you would like to print out. 
=1-10,c1 The DUMPATOMS action with label 
# notice that last atom is a virtual one and will not have
# a correct name in the resulting gro file

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

Click on the labels of the actions for more information on what each action computes

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c1 calculates the position of a virtual atom
DUMPATOMS 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=file.xtc 
ATOMS
the atom indices whose positions you would like to print out. 
=1-10,c1 The DUMPATOMS action with label 

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:

Click on the labels of the actions for more information on what each action computes

c1: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c1 calculates the position of a virtual atom
DUMPATOMS 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=10 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=file.xtc 
ATOMS
the atom indices whose positions you would like to print out. 
=1-10,c1 
PRECISION
The number of digits in trajectory file 
=7 The DUMPATOMS action with label 

Glossary of keywords and components

The atoms involved can be specified using

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

Compulsory keywords

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

Options

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