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Dendrimer Builder Toolkit (DBT)

DBT can be used to build polymer (linear or hyperbranched) in AMBER depending upon multiplicity of joining residues (For more details please see tutorial and refer article: J. Comput. Chem. 2012, 33, 1997-2011). Thus DBT is a graphical user interface (GUI) written in PERL-Tk, which generates a set of commands (xleap/tleap) to be used further by AMBER. DBT has been integrated with AMBER10. DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity and generation of dendrimer.

Please refer:

  • Dendrimer Building Toolkit: Model Building and Characterization of Various Dendrimer Architectures J. Comput. Chem., 2012, 33, 1997-2011
  • System requirements: Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)

    DBT Website

    Equilibrium configurations of G3-G6 PAMAM dendrimers: Here

    Two-phase thermodynamic (2PT) model

    Two-phase thermodynamic (2PT) model is used for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component.

    Please refer:

  • Lin, S.T., Blanco, M. and Goddard III, W.A., 2003. The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids. The Journal of chemical physics, 119(22), pp.11792-11805.
  • Lin, S.T., Maiti, P.K. and Goddard III, W.A., 2010. Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. The Journal of Physical Chemistry B, 114(24), pp.8191-8198.
  • System requirements: Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)

    Please contact us to avail this software.

    TEKMC - Trajectory-Extending Kinetic Monte Carlo

    Please refer:

  • Subhadeep Dasgupta, Arun K. S., K. Ganapathy Ayappa, and Prabal K. Maiti, 2023. Trajectory-Extending Kinetic Monte Carlo Simulations to Evaluate Pure and Gas Mixture Diffusivities through a Dense Polymeric Membrane, J. Phys. Chem. B 2023, 127, 45, 9841–9849.