System configuration
To describe the geometry of the system a configuration file is mandatory. In PumMa this file has the extension .pxf. However, the system configuration file is not only an input file, it also is an output file. For every configuration whose coordinates and velocities are dumped, a system configuration file is generated as well. Therefore, part of the name of the system configuration file is the current iteration, for example IT1250 for iteration 1250. The system configuration file name is always preceded by a base name, which can be set in the input file, see the input options. By default this base name is assumed to be sys. Consequently the very first system configuration file is most likely to be named sysIT0.pxf.
The system configuration file has at least two lines, but the maximum number of lines depends on the number of different type of molecules in the system. As with all other files, blank lines and lines starting with # are ignored. A typical system configuration file for a DPPC bilayer simulation could look like:
SYS BOX 9.345338 9.592250 12.723137 MOL DPPC 128 MOL W 8000
The line starting with the keyword SYS specifies the shape and dimensions of the box. Currently only an orthorhombic box is supported in PumMa, and the only value shape keyword is BOX, which follows the first keyword immediately. The next three arguments give the box dimensions in x-, y- and z-direction (in nm). This declaration can only occur once in the system configuration file.
Besides the box shape line, as many lines as there are molecules are present in the systems configuration file. Every of these lines is indicated by the keyword MOL, followed by the molecule name and the number of molecules of that type in the system. Be aware that this number is not equal to the number of atoms in the system due to the presence of this molecule. In this example there are 128 DPPC molecules in the system, which consist (in the coarse grained model) of 12 atoms each, leading to a total of 1536 atoms associated with the molecule DPPC. Since the molecule W consists of one atom only, the total number of particles in this example system equals 9536.
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