Q is a computer
software
Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work.
...
package for
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of t ...
(MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: ''
empirical valence bond'' (EVB), ''
free energy perturbation
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations.
The FEP method was introduce ...
'' (FEP), and ''linear interaction energy'' (LIE), as well as, more recently, also
path integral calculations using the bisection quantum classical path (BQCP) approach.
The methods in which the program specializes can return quantitative calculations of the energy balance which occurs in
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
s 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 being force-field agnostic, meaning that it provides no force-field, but can rather use common force-fields such as
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHA ...
,
AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In ...
,
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.
Functional form
The functional form of the OPLS force field is very similar to tha ...
, 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
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 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.
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 nonbonded interactions such as
van der Waals force
In molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and th ...
and
electrostatics interactions in detail on the
solvent
A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for ...
, the
solution
Solution may refer to:
* Solution (chemistry), a mixture where one substance is dissolved in another
* Solution (equation), in mathematics
** Numerical solution, in numerical analysis, approximate solutions within specified error bounds
* Soluti ...
, 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.
External links
* {{Official website, xray.bmc.uu.se/~aqwww/q
Molecular dynamics software