Bruccoleri came up with the name HARMM (HARvard Macromolecular Mechanics), but it seemed inappropriate. So they added a C for Chemistry. Karplus said: "I sometimes wonder if Bruccoleri's original suggestion would have served as a useful warning to inexperienced scientists working with the program." CHARMM has continued to grow and the latest release of the executable program was made in 2015 as CHARMM40b2. Running CHARMM under Unix-Linux The general syntax for using the program is: charmm -i filename.inp -o filename.out charmm – The name of the program (or script which runs the program) on the computer system being used. filename.inp – A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and 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. filename.out – 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. Volunteer computing Docking@Home, hosted by University of Delaware, one of the projects which use an open-source platform for the distributed computing, BOINC, used CHARMM to analyze the atomic details of protein-ligand interactions in terms of molecular dynamics (MD) simulations and minimizations. World Community Grid, sponsored by IBM, ran a project named The Clean Energy Project which also used CHARMM in its first phase which has completed. See also References External links , with documentation and helpful discussion forums , BIOVIA CHARMM tutorial MacKerell website, hosts package of force field parameters for CHARMM C.Brooks website CHARMM page at Harvard Roux website Bernard R. Brooks Group website Docking@Home CHARMM-GUI project CHARMMing (CHARMM Interface and Graphics) CHARMM Tutorial Molecular dynamics software Force fields Fortran software Harvard University