Action: DUMPMASSCHARGE

Module	generic
Description	Usage
Dump masses and charges on a selected file.
This action outputs data to a file. You can read more about how PLUMED manages output files here

Details and examples

Dump masses and charges on a selected file.

This command dumps a file that contains charges and masses of the atoms. The following example shows how it is used:

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

c1The COM action with label c1 calculates the following quantities:
 Quantity   
 Type   
 Description  
c1
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1-10
c2The COM action with label c2 calculates the following quantities:
 Quantity   
 Type   
 Description  
c2
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11-20
DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=c1,c2 FILEfile on which to output coordinates; extension is automatically detected=coms.xyz STRIDE the frequency with which the atoms should be output=100

The DUMPATOMS action with label  calculates somethingDUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mcfile

The DUMPMASSCHARGE command only outputs the masses and charges once in the simulation (during the first step).

Output the masses and charges in this way is useful if you want to do some postprocessing that relies on knowing the masses and charges of atoms. To use the mcfile tht is output by the command above you would use the following driver command to read in the charges and masses from the mcfile.

plumed driveranalyze trajectories with plumed This action has hidden defaults. More details --mcprovides a file with masses and charges as produced with DUMPMASSCHARGE mcfile --plumed specify the name of the plumed input file plumed.dat --ixyzthe trajectory in xyz format traj.xyz

The driver action with label plumed calculates somethingplumed driveranalyze trajectories with plumed This action uses the defaults shown here. More details --mcprovides a file with masses and charges as produced with DUMPMASSCHARGE mcfile --plumed specify the name of the plumed input file plumed.dat --ixyzthe trajectory in xyz format traj.xyz
 --timestep the timestep that was used in the calculation that produced this trajectory in picoseconds 1.0 --trajectory-stride the frequency with which frames were output to this trajectory during the simulation (0 means that the number of the step is read from the trajectory file, currently working only for xtc/trr files read with --ixtc/--trr) 1 --multi set number of replicas for multi environment (needs MPI) 0 --dump-forces-fmt the format to use to dump the forces %%f 

DUMPMASSCHARGE outputs the masses of all the atoms by default. However, if you want to write the masses and charges for a particular subset of the atoms you can use the ATOMS keyword as illustrated in the example input below:

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

solute_ionsThe GROUP action with label solute_ions calculates the following quantities:
 Quantity   
 Type   
 Description  
solute_ions
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-121,200-2012
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=traj.gro ATOMSthe atom indices whose positions you would like to print out=solute_ions STRIDE the frequency with which the atoms should be output=100
The DUMPATOMS action with label  calculates somethingDUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mcfile ATOMSthe atom indices whose charges and masses you would like to print out=solute_ions

Notice, also, that you can print the masses and charges on separate files by using the ONLY_MASSES and ONLY_CHARGES flags as shown below:

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

DUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=mfile ATOMSthe atom indices whose charges and masses you would like to print out=1-100 ONLY_MASSES Only output masses to file
The DUMPMASSCHARGE action with label  calculates somethingDUMPMASSCHARGEDump masses and charges on a selected file. More details FILEfile on which to output charges and masses=qfile ATOMSthe atom indices whose charges and masses you would like to print out=1-100 ONLY_CHARGES Only output charges to file

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ATOMS	atoms	the atom indices whose charges and masses you would like to print out

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	input	none	the atom indices whose charges and masses you would like to print out
FILE	compulsory	none	file on which to output charges and masses
ONLY_MASSES	optional	false	Only output masses to file
ONLY_CHARGES	optional	false	Only output charges to file