The Bresme Group (@bresmegroup)
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1

Atomistic_Nodal_Approach_Nanoparticles

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 workflow to illustrate the process of obtaining interfacial thermal conductance in the 'cube.ipynb' file.
Jupyter Notebook
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2

SAP_bare-protein

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
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3

Buffer-SAP_BSAP

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
3
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4

IntegrateProfile

Cumulative integration over multiple LAMMPS ave/chunk .profile files
Python
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5

MARTINI3_Free_Histidine

GROMACS format MARTINI3 parameter files for free histidine in solution (+1 and neutral charge states)
1
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6

SAP-Protein-in-Histidine-Buffer

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
1
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