Input files
In order to be able to start a simulation with PumMa a set of input files need to be present. This set includes a file containting all the input options (such as the temperature of the system, the number of time steps to be performed and so on) and furthermore a force field parameter file, a system configuration file, and as many topology and coordinate files as there are types of molecules in the system. When necessary some special tasks can be employed, such as fixing atoms.
A typical set of input files is called input.pif, the input option file, parameters.ppf, the parameter file, sysIT0.pxf the configuration file, *.ptf the topology file for each molecule (hence the wildcard character *) and the coordinate file *.pcf. The file extension is always of the form .p*f, where the wildcard character indicates whether it is an input (i), output (o), parameter (p), topology (t) or coordinate (c) file.
This manual starts of with the discussion of all input options available to PumMa, but even before that a short introduction on reduced units is given, including a conversion tool.
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