Q (software)

Q is a Molecular Dynamics (MD) simulation package which, unlike other MD codes, has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the Empirical Valence Bond (EVB) approach, the Free Energy Perturbation (FEP) method, and the Linear Interaction Energy (LIE) method.

The three methods that the program specializes on can return quantitative calculations of the energetic 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 (Lind et al. 2013), or details in enzymatic reactions (Mones et al. 2013) among others.

The program is similar to gromacs in the sense that it's force-field agnostic, meaning that it does not provide a force-field itself, but it 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 (to prepare input files from X-ray coordinates), qfep (to process MD calculations for FEP) and others.

General command to run Q

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.out

qdyn 

This is the name of the main program which runs dynamics.

inputfile.inp 

This is text file which specifies all options to the program such as how long the simulation is, how long are the time-steps, what temperature is being simulated and many others.

filename.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 non-bonded interactions such as van der Waals and electrostatic interactions in detail on the solvent, the solute, and the interactions among them.

See also

References

• Marelius J., Kolmodin K., Feierberg I. and Åqvist J., (1998). "Q: A Molecular Dynamics Program for Free Energy Calculations and Empirical Valence Bond Simulations in Biomolecular Systems", Journal of Molecular Graphics and Modelling, 16, 213-225.

• Lind C., Sund J. and Åqvist J., (2013). "Codon-reading Specificities of Mitochondrial Release Factors and Translation Termination at Non-standard Stop Codons", Nature Communications, 4,2940.

• Mones L., Tang W., and Florian J., (2013). "Empirical Valence Bond Simulations of the Chemical Mechanism of ATP to cAMP Conversion by Anthrax Edema Factor", Biochemistry', 52, 2672-2682.