FFEA Input File

In this section we describe the structure of the .ffea file. The complete reference to all the keywords describing the system can be found here. More information on every simulation approach will be found in the corresponding pages.

Input file syntax

The input file has two main blocks:

• param: describing global parameters of the system
• system: describing the system itself.

Blocks open with: <block> and closed with </block>, and the structure of a minimal valid .ffea file looks like:

<param>
  ...
</param>

<system>
    <blob>
     ... 
    </blob>
</system>     

where:

• the <param> block contains parameters affecting the whole system.
• the <system> block contain subblocks describing the blobs and possibly their interactions.
• each blob block defines a protein in the simulation

Attributes within blocks are defined between < >, using International System Units. For example, temperature is set to 300K using kT, as:

<kT = 4.11e-21>

The simulation length is set using num_steps and will be cast to an integer:

<num_steps = 1e8>

File names can be written relative to the directory where the .ffea script resides, or giving an absolute path:

<trajectory_out_fname = /path/to/your/file/trajectory.out>

Comments are allowed when enclosed between <!-- and --> signs, e. g. <!-- this is a comment :) -->.

A minimal input file is generated automatically through voltoffea, the next sections describe how to set up more complex systems, and all the keywords and blocks are listed and described in the reference site.