Editing CHARMM (section)

== Running CHARMM under Unix-Linux ==
The general syntax for using the program is:

<code>charmm -i filename.inp -o filename.out</code>

* <code>charmm</code> – The name of the program (or script which runs the program) on the computer system being used.
* <code>filename.inp</code> – A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and [[Force field (chemistry)|force field]] (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files). One can then modify the molecules (adding hydrogens, changing secondary structure). The calculation section can include energy minimization, dynamics production, and analysis tools such as motion and energy correlations.
* <code>filename.out</code> – The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications. The values for temperature, energy pressure, etc. are output at that frequency.