5.2 Large Systems Studies Using Classical Dynamics
167
This has fostered the assemblage and development of several popular computer codes
designed for classical (and SC) mechanics studies.
Among the most popular codes of this type are:
VENUS96 [110] a program in continuous development by W.L. Hase of the
Technical University of Texas that calculates classical trajectories and resulting
detailed probabilities, cross section and rate coefficients of colliding bodies (atoms
and/or molecules) by integrating related Hamilton equations in cartesian coordinates.
VENUS96 discretizes the probabilities using approximate means and can be easily
linked to programs performing an SC-IVR evaluation of state-to-state probabilities.
SC-IVR [111] a semiclassical initial value representation program based on the
outcome of a classical trajectory package used to calculate the discrete spectrum of
medium size molecules and other state-to-state transition properties.
DL_POLY [112] a popular code for the integration of the classical equations
of motion of molecular dynamics. It is a general purpose package of subroutines,
programs, and data designed to facilitate molecular dynamics simulations. DL_POLY
is continually developed at Daresbury Laboratory by W. Smith and I.T. Todorov under
the auspices of the British EPSRC and NERC in support of the CCP5 program.
It can be used to simulate a wide variety of molecular systems including simple
liquids, ionic liquids and solids, small polar and nonpolar molecular systems, bioand synthetic polymers, ionic polymers and glasses solutions, simple metals, and
alloys.
GROMACS [113] is a versatile molecular dynamics package integrating the Newton equations of motion for systems with hundreds to millions of particles. It has been
used in a large number of case studies and it consists of a complete workflow aimed
at exploiting the interoperability within a local cluster platform (HPC capable) and a
worldwide distributed computing infrastructure (DCI) as will be described in some
detail later in this chapter). In the workflow, the possibility of coupling the run of
different jobs is taken care by means of links (semaphores) defining the dependency
job chain.
NAMD [114] is a parallel molecular dynamics code designed for highperformance simulations of large biomolecular systems and it has been used to study
the behavior of a lipidic bilayer in water. Ported on the distributed environments
using OpenMPI parallel libraries, a direct acyclic graph (DAG) has been implemented to run the code in a semiautomatic way and facilitate the user to carry out
his/her calculations.
AutoDock [115] is a suite of automated docking tools. It is designed to predict
how small molecules, such as substrates or drug candidates, bind to a receptor of a
known 3D structure. Current distributions of AutoDock consist of two generations of
software: AutoDock 4 and AutoDock Vina. AutoDock 4 actually consists of two main
programs: autodock performs the docking of the ligand to a set of grids describing
the target protein; autogrid precalculates these grids. In addition to using them for
docking, the atomic affinity grids can be visualized. This can help, for example,
to guide organic synthetic chemists to design better binders. AutoDock Vina does
not require choosing atom types and precalculating grid maps for them. Instead, it
rapidly calculates the grids internally, for the types of atoms needed.
167
This has fostered the assemblage and development of several popular computer codes
designed for classical (and SC) mechanics studies.
Among the most popular codes of this type are:
VENUS96 [110] a program in continuous development by W.L. Hase of the
Technical University of Texas that calculates classical trajectories and resulting
detailed probabilities, cross section and rate coefficients of colliding bodies (atoms
and/or molecules) by integrating related Hamilton equations in cartesian coordinates.
VENUS96 discretizes the probabilities using approximate means and can be easily
linked to programs performing an SC-IVR evaluation of state-to-state probabilities.
SC-IVR [111] a semiclassical initial value representation program based on the
outcome of a classical trajectory package used to calculate the discrete spectrum of
medium size molecules and other state-to-state transition properties.
DL_POLY [112] a popular code for the integration of the classical equations
of motion of molecular dynamics. It is a general purpose package of subroutines,
programs, and data designed to facilitate molecular dynamics simulations. DL_POLY
is continually developed at Daresbury Laboratory by W. Smith and I.T. Todorov under
the auspices of the British EPSRC and NERC in support of the CCP5 program.
It can be used to simulate a wide variety of molecular systems including simple
liquids, ionic liquids and solids, small polar and nonpolar molecular systems, bioand synthetic polymers, ionic polymers and glasses solutions, simple metals, and
alloys.
GROMACS [113] is a versatile molecular dynamics package integrating the Newton equations of motion for systems with hundreds to millions of particles. It has been
used in a large number of case studies and it consists of a complete workflow aimed
at exploiting the interoperability within a local cluster platform (HPC capable) and a
worldwide distributed computing infrastructure (DCI) as will be described in some
detail later in this chapter). In the workflow, the possibility of coupling the run of
different jobs is taken care by means of links (semaphores) defining the dependency
job chain.
NAMD [114] is a parallel molecular dynamics code designed for highperformance simulations of large biomolecular systems and it has been used to study
the behavior of a lipidic bilayer in water. Ported on the distributed environments
using OpenMPI parallel libraries, a direct acyclic graph (DAG) has been implemented to run the code in a semiautomatic way and facilitate the user to carry out
his/her calculations.
AutoDock [115] is a suite of automated docking tools. It is designed to predict
how small molecules, such as substrates or drug candidates, bind to a receptor of a
known 3D structure. Current distributions of AutoDock consist of two generations of
software: AutoDock 4 and AutoDock Vina. AutoDock 4 actually consists of two main
programs: autodock performs the docking of the ligand to a set of grids describing
the target protein; autogrid precalculates these grids. In addition to using them for
docking, the atomic affinity grids can be visualized. This can help, for example,
to guide organic synthetic chemists to design better binders. AutoDock Vina does
not require choosing atom types and precalculating grid maps for them. Instead, it
rapidly calculates the grids internally, for the types of atoms needed.