System description

To be able to review the system settings after the simulation has finished, PumMa generates as system description file containing all simulation settings. This allows the user to check for possible errors or to review certain settings. The name of this file, sysdescr.txt is fixed. The file basically consists of three parts.

The first part informs the user about the general system settings. For instance the number of particles and the number of atoms, bonds, angles, and so on, within a molecule type. An example of such information block is

  Simulation parameters and system description 'sys'
  System consists of 9399 particles
  System consists of 2 molecule types:
    6471 W molecules each having 1 atoms, 0 bonds, 0 bendings, 0 torsions, 
         and 0 impropers
    244 G4T4T4 molecules each having 12 atoms, 11 bonds, 4 bendings, 
         0 torsions, and 0 impropers

The second part of the sysdescr.txt file consists of the so-called Lennard-Jones information table. It lists all non-bonded interaction pairs and their constants. For example:

  Lennard-Jones Information Table:
               epsij    sigij    rcij     rlij      LJshfij
    G G (0 0) 3.932960 0.449975 1.124938 1.529915 -0.008022
    T G (1 0) 1.966480 0.449975 0.505080 0.910058 -0.491620
    T T (1 1) 1.966480 0.449975 1.124938 1.529915 -0.008022
    W G (2 0) 3.932960 0.455387 1.138468 1.543446 -0.008022
    W T (2 1) 1.966480 0.455387 0.511155 0.916133 -0.491620
    W W (2 2) 3.932960 0.460800 1.151999 1.556976 -0.008022

The first two arguments give the atom types for the non-bonded interaction and the two numbers between brackets the internal atom type numbers. Next the well depth (epsij, kJ/mol in the Lennard-Jones equation) of this interaction is given, followed by the collision diameter (sigij, the σ of the Lennard-Jones equation) for this interaction (which is derived through the Lorentz-Berthelot mixing rules). Subsequently the cut-off radius (rcij in nm) of this interaction pair is given followed by the maximum radius for the pair list (rlij, also in nm). The last value (LJshfij is the amount of energy (in kJ/mol) that has to be subtracted from the potential energy in order to keep the potential continuous at the cut-off point.

The last part of the system description file contains all the input options as could have been set in the input options file. It shows not only values that have been specified explicitly in the input file, but also options that remain at their default value, as well as some options that the user cannot control, but are interesting enough to be reported. An excerpt of this part might look like

  Simulation Parameters (default or from input.pif)
    Requested start time step [IT]   = 0
    Requested end time step [max_IT] = 500000
    Requested time step size [Dt]    = 0.012000 ps
    ...

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