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Input and Output Files

2 is designed to be an easily applicable simulation tool. The structure of the input files as well as the output files is shown schematically.

Input files

The simulation tool ms2 requires one input file (*.par) to specify the simulation parameters and one molecular model file  (*.pm) for every molecular species considered.
The *.par file contains all input variables for the simulation process such as simulation type, ensemble, number of equilibration and production steps, time step length, and many more. Furthermore, the user can specify temperature, density and fluid composition. All options with a detailed description and an example can be found here.
Its composition is facilitated by the ms2 feature program ms2par. Its use is described in detail in the section "Feature programs".
A *.pm file contains the molecular model for a given substance. It contains the parameters and relative position of all sites. An example for a *.pm file with a description of all variables is given in the paper and here.

Output files

ms2 yields seven output files:
*.log file - stores a complete summary of all the steps taken by ms2.
*.res file - contains the results of the simulation in an aggregated form. The data is written to file in reduced quantities as well as in SI units, along with the statistical uncertainties of the calculated properties. The *.res file is created during simulation and updated every specified number of time steps or cycles.
*.run file - contains the calculated properties of the simulation for a specified  time step or cycle interval. The file is in tabular form, where the data is given in reduced units. The file is subsequently updated according to the user specification, which is set in the *.par file.
· *.rav file - contains the running averages of simulation properties. The block size and therefore the number of output lines in the *.rav file is user defined and can be set in the *.par file.
*.rtr file - stores the final value of the autocorrelation function and its integral. The number of output lines can be defined in the *.par file.
*.rst file - is the restart file of the simulation. It contains all molecular positions, velocities, orientations, forces and block averages for the thermodynamic properties. It is written once at the end of the simulation or immediately after having received a termination signal of the operating system. The restart file allows for a stepwise execution of the simulation, necessary e.g. in case of an early interuption of the simulation, time limits on a queuing system, or unexpected halts.
*.vim file - is a visualization file. It contains the positions and orientations of all molecules in an aggregated ASCII-form. The configurations are written to file after a user-specified interval of time steps or cycles. The *.vim file is readable by the visualization tool ms2molecules, which is also part of the simulation package and described in section "Feature programs".
*.nrm file - stores the coordinates of the molecule after principal axis transformation.