DUMPMASSCHARGE

This is part of the generic module

Dump masses and charges on a selected file.

This command dumps a file containing charges and masses. It does so only once in the simulation (at first step). File can be recycled in the driver tool.

Notice that masses and charges are only written once at the beginning of the simulation. In case no atom list is provided, charges and masses for all atoms are written.

Examples

You can add the DUMPMASSCHARGE action at the end of the plumed.dat file that you use during an MD simulations:

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. 
=1-10 The COM action with label c1 calculates the following quantities:

 Quantity   
 Description  
c1.x
the x coordinate of the virtual atom
c1.y
the y coordinate of the virtual atom
c1.z
the z coordinate of the virtual atom
c1.mass
the mass of the virtual atom
c1.charge
the charge of the virtual atom


c2: COM 
ATOMS
the list of atoms which are involved the virtual atom's definition. 
=11-20 The COM action with label c2 calculates the following quantities:

 Quantity   
 Description  
c2.x
the x coordinate of the virtual atom
c2.y
the y coordinate of the virtual atom
c2.z
the z coordinate of the virtual atom
c2.mass
the mass of the virtual atom
c2.charge
the charge of the virtual atom


DUMPATOMS 
ATOMS
the atom indices whose positions you would like to print out. 
=c1,c2 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=coms.xyz 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=100 The DUMPATOMS action with label 
DUMPMASSCHARGE 
FILE
compulsory keyword 
file on which to output charges and masses. 
=mcfile The DUMPMASSCHARGE action with label 

In this way, you will be able to use the same masses while processing a trajectory from the driver . To do so, you need to add the –mc flag on the driver command line, e.g.

plumed driver --mc mcfile --plumed plumed.dat --ixyz traj.xyz

With the following input you can dump only the charges for a specific group:

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

solute_ions: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group. 
=1-121,200-2012 The GROUP action with label solute_ions defines a group of atoms so that they can be referred to later in the input
DUMPATOMS 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=traj.gro 
ATOMS
the atom indices whose positions you would like to print out. 
=solute_ions 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the atoms should be output 
=100 The DUMPATOMS action with label 
DUMPMASSCHARGE 
FILE
compulsory keyword 
file on which to output charges and masses. 
=mcfile 
ATOMS
the atom indices whose charges and masses you would like to print out. 
=solute_ions The DUMPMASSCHARGE action with label 

Glossary of keywords and components

The atoms involved can be specified using

ATOMS

the atom indices whose charges and masses 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 charges and masses.

Options

ONLY_MASSES	( default=off ) Only output masses to file
ONLY_CHARGES	( default=off ) Only output charges to file