This is part of the multicolvar module

Dump atom positions and multicolvar on a file.

Examples

In this examples we calculate the distances between the atoms of the first and the second group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the coordinates of their geometric center and their distance.

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

pos: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =220,221,235,236,247,248,438,439,450,451,534,535 The GROUP action with label pos defines a group of atoms so that they can be referred to later in the input
neg: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =65,68,138,182,185,267,270,291,313,316,489,583,621,711 The GROUP action with label neg defines a group of atoms so that they can be referred to later in the input
slt: DISTANCES GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=pos GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=neg The DISTANCES action with label slt
DUMPMULTICOLVAR DATAcompulsory keyword 
certain actions in plumed work by calculating a list of variables and summing over
them. =slt FILEcompulsory keyword 
file on which to output coordinates =MULTICOLVAR.xyz The DUMPMULTICOLVAR action with label

(see also DISTANCES)

Glossary of keywords and components

The atoms involved can be specified using

ORIGIN

You can use this keyword to specify the position of an atom as an origin. The positions output will then be displayed relative to that origin. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

DATA	certain actions in plumed work by calculating a list of variables and summing over them. This particular action can be used to calculate functions of these base variables or prints them to a file. This keyword thus takes the label of one of those such variables as input.
STRIDE	( default=1 ) the frequency with which the atoms should be output
FILE	file on which to output coordinates
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