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NAMD requires a number of input files to run. These include:
Details about the supported format of these input files can be found in the NAMD User's Guide.
NAMD supports several running modes. In the simplest case, it can be run in serial mode by typing:
where config_file is the configuration input file mentioned above. It is recommended to give the configuration file the file extension .namd to enable consistent naming of the output files. These will be generated automatically, and the progress of the program run will be tracked on the screen.
NAMD is also able to run in parallel mode. For our shared-memory systems, it is easiest to run it by specifying the number of threads through the +p option:
namd2 +pN config_file
if N threads are requested.