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    11 repositories

    • Supplementary-information-files

      Public
      This repository contains supplementary information flles
      0•0•0•0•Updated Sep 8, 2024Sep 8, 2024

    • Bash-scripts

      Public
      Bash scripts for file processing
      Shell
      •0•0•0•0•Updated May 10, 2024May 10, 2024

    • Python-Scripts

      Public
      Python
      •0•0•0•0•Updated Oct 30, 2023Oct 30, 2023

    • Buffer-SAP_BSAP

      Public
      Set of FORTRAN codes and script files for the calculation of Spatial Aggregation Propensity (SAP) of proteins (including the effect of buffer histidine on the solvent accessible area of the protein) from GROMACS MD trajectories. The scripts use GROMACS analysis code gmx to calculate the solvent accessible surface area.
      Fortran
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Apr 9, 2022Apr 9, 2022

    • MARTINI3_Free_Histidine

      Public
      GROMACS format MARTINI3 parameter files for free histidine in solution (+1 and neutral charge states)
      GNU General Public License v3.0
      •1•1•0•0•Updated Apr 9, 2022Apr 9, 2022

    • SAP-Protein-in-Histidine-Buffer

      Public
      Set of FORTRAN codes and script files for the calculation of Spatial Aggregation Propensity (SAP) of proteins (including the effect of buffer histidine on protein structure) from GROMACS MD trajectories. The scripts use GROMACS analysis code gmx to calculate the solvent accessible surface area.
      Fortran
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 9, 2022Apr 9, 2022

    • SAP_bare-protein

      Public
      Set of FORTRAN codes and script files for the calculation of Spatial Aggregation Propensity (SAP) of of bare proteins from GROMACS MD trajectories. The scripts use GROMACS analysis code gmx to calculate the solvent accessible surface area.
      Fortran
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Apr 9, 2022Apr 9, 2022

    • multipole-parakeet

      Public
      A MD Analysis Class for calculating the charge, dipole and quadrapole density distributions
      Python
      •1•0•0•0•Updated Feb 1, 2022Feb 1, 2022

    • Atomistic_Nodal_Approach_Nanoparticles

      Public
      Python Code for Processing LAMMPS Data generated for two data types: LAMMPS trajectory file and LAMMPS dump files. Subsequently, the code involves post-processing of the data to give interfacial heat flux, temperature discontinuity and ultimately interfacial conductance using the atomistic nodal approach. Pythode code is also presented as a work…
      simulationmolecular-dynamicsthermodynamicslammpsnanoparticlesconductance
      Jupyter Notebook
      •2•6•0•0•Updated Oct 1, 2021Oct 1, 2021

    • janus-spatial-control

      Public
      MATLAB
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

    • IntegrateProfile

      Public
      Cumulative integration over multiple LAMMPS ave/chunk .profile files
      Python
      •0•2•1•0•Updated Jul 14, 2017Jul 14, 2017