Getting Started

To run PLUMED you need to provide one input file.

You can follow the PLUMED Masterclass 21.1: PLUMED syntax and analysis to learn more about it.

In this input file you specify what it is that PLUMED should do during the course of the run. Typically this will involve calculating one or more collective variables, perhaps calculating a function of these CVs and then doing some analysis of values of your collective variables/functions or running some free energy method. A very brief introduction to the syntax used in the PLUMED input file is provided in this 10-minute video .

Within this input file every line is an instruction for PLUMED to perform some particular action. This could be the calculation of a colvar, an occasional analysis of the trajectory or a biasing of the dynamics. The first word in these lines specify what particular action is to be performed. This is then followed by a number of keywords which provide PLUMED with more details as to how the action is to be performed. These keywords are either single words (in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic boundary conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated list with no spaces of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in the calculation of a particular colvar). The reason why spaces are not admitted is that PLUMED should be able to understand when the list of atoms ended and a new keyword should be expected. Space separated lists can be used instead of comma separated list if the entire list is enclosed in curly braces (e.g. ATOMS={1 2 3 4}). Please note that you can split commands over multiple lines by using Continuation lines.

The most important of these keywords is the label keyword as it is only by using these labels that we can pass data from one action to another. As an example if you do:

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

DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label 

Then PLUMED will do nothing other than read in your input file. In contrast if you do:

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

d1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d1 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10 The PRINT action with label 

then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions as long as it does not begin with the symbol @. Strings beginning with @ are used by within PLUMED to reference special, code-generated groups of atoms and to give labels to any Actions for which the user does not provide a label in the input.

Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically removes it and adds an equivalent label (LABEL=pippo). Thus, a completely equivalent result can be obtained with the following shortcut:

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

d1: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=1,2 The DISTANCE action with label d1 calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=d1 
FILE
the name of the file on which to output these quantities 
=colvar 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=10 The PRINT action with label 

Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define one or more value, which can be then referred using the corresponding label.

Actions can be referred also with POSIX regular expressions (see Regular Expressions) if regex library is available on your system and detected at configure time. You can also add Comments to the input or set up your input over multiple files and then create a composite input by Including other files.

More information on the input syntax as well as details on the the various trajectory analysis tools that come with PLUMED are given in:

• Collective Variables tells you about the ways that you can calculate functions of the positions of the atoms.
• Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
• Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.

Plumed units

By default the PLUMED inputs and outputs quantities in the following units:

• Energy - kJ/mol
• Length - nanometers
• Time - picoseconds

Unlike PLUMED 1 the units used are independent of the MD engine you are using. If you want to change these units you can do this using the UNITS keyword.