Tag: Molecular Dynamics

MDynaMix 5.2.8 – Molecular Dynamics Program

MDynaMix 5.2.8

:: DESCRIPTION

MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell. Rigid bonds are constrained by the SHAKE algorithm. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are implemented, as well as Ewald sum for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the Path Integral Molecular Dynamics approach. Possibility for free energy computations by the expanded ensemble method is included.

::DEVELOPER

Lyubartsev, Alexander

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MDynaMix

:: MORE INFORMATION

Citation

A.P.Lyubartsev, A.Laaksonen,
MDynaMix – A scalable portable parallel MD simulation package for arbitrary molecular mixtures”
Computer Physics Communications, 128, 565-589 (2000).

RIP 1.1 – Accelerated Molecular Dynamics

RIP 1.1

:: DESCRIPTION

RIP (Rotamerically Induced Perturbation) generates local perturbations of residues in a protein. In picoseconds of a molecular-dynamics (MD) simulation, RIP generates motions that reveal certain mechanical properties of a protein. 1) Flexibility Analysis: using larger perturbations, RIP can induce several ?ngstroms of conformational change in loops, identifying potential allosteric effectors. E.g. on the right is the RIP perturbation on TRP-83 in the Ligand-Binding Domain of the Estrogen Receptor, which produces a dramatic 10 ? motion of the ligand-binding Helix 12 in a 10 ps simulation. 2) Coupling Analysis: using small RIP perturbations, residues that interact strongly can be identified. Analysis of the patterns of strongly interacting residues allows an analysis of tertiary structure dynamics.

::DEVELOPER

Bosco K. Ho

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RIP

:: MORE INFORMATION

Reference for Flexibility Analysis: “Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations” by Bosco K. Ho and David A. Agard. PLoS Comput Biol (2009) 5(4): e1000343.

Reference for Coupling Analysis: “Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility“by Bosco K. Ho and David A. Agard. Protein Science (2010) 19:398-411.

MDLab – Molecular Dynamics Simulation Prototyping Environment

MDLab

:: DESCRIPTION

MDLab (MDL) is a user-friendly environment for prototyping molecular dynamics simulation protocols and numerical methods, built with the scripting language Python. Our goal is to provide developers of propagator scheme and force computation algorithms with (1) mathematical syntax which enables them to develop these methods using array and matrix operations, and (2) a set of domain-specific libraries which enable testing and debugging of these methods using real biological systems.

::DEVELOPER

Izaguirre Lab at Notre Dame

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MDLab

:: MORE INFORMATION

Citation

T. Cickovski, S. Chatterjee, A. Wenger, C. Sweet and J. A. Izaguirre.
MDLab: A Molecular Dynamics Simulation Prototyping Environment.
J Comput Chem. 2010 May;31(7):1345-56.

ProtoMol 3.3 – Molecular Dynamics (MD) Simulation

ProtoMol 3.3

:: DESCRIPTION

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.

::DEVELOPER

ProtoMol Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • perl/tk

:: DOWNLOAD

 ProtoMol

:: MORE INFORMATION

Citation

T. Matthey, T. Cickovski, S. S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach, and J. A. Izaguirre.
ProtoMol: An object-oriented framework for prototyping novel algorithms for molecular dynamics.
ACM Trans. Math. Softw., 30(3):237-265 (2004)

MD Morphing 1.0 – Perform Molecular Dynamics Morphing Simulations

MD Morphing 1.0

:: DESCRIPTION

MD Morphing software is able to generate pathways connecting two conformation states by MD simulations with morphing constraint potentials. It provide a tool to sample between multiple conformation states of complex bio-molecular systems.

::DEVELOPER

MD Morphing Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

 MD Morphing

:: MORE INFORMATION