Q (software)
Q is a computer software package for molecular dynamics simulation. Unlike other MD codes, it has specialized since its conception on three specific types of free energy calculations. These calculations are based on the methods: empirical valence bond, free energy perturbation, and linear interaction energy, as well as, more recently, also path integral calculations using the bisection quantum classical path approach.
The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in proteins and nucleic acids. It can provide insight into key problems in biochemistry such as, energetic details on parts of the translation mechanism in mitochondrial ribosomes, or details in enzymatic reactions, among others.
The program is similar to GROMACS in being force-field agnostic, meaning that it provides no force-field, but can rather use common force-fields such as CHARMM, AMBER, OPLS, and GROMOS.
The software provides one main utility for molecular dynamics called qdyn, and various subprograms such as qprep, qfep, and others.
General command to run
The general command to run Q is very similar to that of other MD programs and its syntax for a dynamics run is as follows:qdyn inputfile.inp > outputfile.outqdyn – This is the name of the main program which runs dynamics.inputfile.inp – This is a text file which specifies all options to the program such as how long are the simulation and the time-steps, what temperature is being simulated, and many others.outputfile.out – This is the output file which gives a detailed account of the energetic results. The verbosity of the information in the output file is controlled in the input file. The output places emphasis on reporting on nonbonded interactions such as van der Waals force and electrostatics interactions in detail on the solvent, the solution, and the interactions among them.