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@soft-matter-theory-at-icmab-csic Soft Matter Theory at ICMAB-CSIC

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    28 repositories

    • TFG_Mario_Martinez

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • Mucus-and-coronavirus

      Public
      Data files of mucus and the SARS-CoV-2 virus and input file for running the simulation in LAMMPS
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 25, 2025Apr 25, 2025

    • Hydrogel-LAMMPS

      Public
      Structure and input files of the hydrogel model
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 12, 2025Apr 12, 2025

    • Coronavirus-envelope-with-M-protein

      Public
      Coordinate files of the SARS-CoV-2 viral envelope
      Apache License 2.0
      •0•0•0•0•Updated Apr 8, 2025Apr 8, 2025

    • COSAN

      Public
      Data (topology, structures, forcefields,...) corresponding to our simulations of COSAN Cobalt bis(dicarbollide) anion
      Fortran
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jan 14, 2025Jan 14, 2025

    • Graphene_DFT_water_ions_AS

      Public
      DFT Calculations showing optimized structures of water ions near graphene as published
      1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • spike_surface_electrostatics

      Public
      This repository contains sample data files for PyGBe electrostatic calculations of Spike SARS-CoV-2 proteins and charged surfaces.
      GLSL
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • TFG_Gabriel_Heparin_MD

      Public
      Computational simulation of heparin and its electrostatic interaction with ions for hydrogel design
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 24, 2024Jun 24, 2024

    • Native-contacts-determination-from-MD

      Public
      We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU approach (http://pomalab.ippt.pan.pl/GoContactMap/).
      Tcl
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jun 13, 2024Jun 13, 2024

    • tfg_Fenics_Susana_Merce

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • pygbe_tutorial

      Public
      Configuration files and results for PyGBe calculations
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Feb 1, 2024Feb 1, 2024

    • chitin_builder

      Public
      Chitin builder: A code to build chitin atomistic structures in Visual Molecular Dynamics (VMD)
      vmdmdchitin
      Rich Text Format
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Jan 30, 2024Jan 30, 2024

    • VSV-G

      Public
      Interaction of VSV-G protein and heparin
      Apache License 2.0
      •0•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • anticancer-drug-KRAS4B-G12D

      Public
      Files for MD simulation of the interactions between drug LIG1 and oncogenic KRAS4B G12D mutant anchoring to cell membrane
      Tcl
      •0•1•0•0•Updated Nov 22, 2023Nov 22, 2023

    • tfg_biofisica_Adrian_Gracia

      Public
      Archivos utilizados para la realización de mi Trabajo de Fin de Grado en Física.
      Python
      •1•0•0•0•Updated Aug 18, 2023Aug 18, 2023

    • TFG_Toha_2023

      Public
      TFG project by Ariadna Toha at our group (2022/2023)
      Python
      •1•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • TFG-Joan

      Public
      TFG Joan Tibau sobre ML i simulacions moleculars
      Jupyter Notebook
      •1•0•0•0•Updated Jun 28, 2023Jun 28, 2023

    • TFG-Maximilia-Soler

      Public
      TFG Maximilia Soler Grau en Fisica UAB supervisat per Jordi Faraudo a ICMAB-CSIC
      M4
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 14, 2023Jun 14, 2023

    • TFG-ML-Statistical-Physics

      Public
      TFG Joaquim Tarin Oliva Physics UAB
      Jupyter Notebook
      •2•0•0•0•Updated Jun 13, 2023Jun 13, 2023

    • solvents_for_VMD

      Public
      Datafiles for solvating with VMD with typical solvents different than water
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • surfactants-coronavirus-AA

      Public
      Files for the coarse-grained and all-atom simulations between SARS-CoV-2 virus and surfactants
      0•0•0•0•Updated Feb 3, 2023Feb 3, 2023

    • CG_Martini_Quatsome

      Public
      Data corresponding to CG simulations of Quatsome vesicles using Martini CG forcefield
      0•0•0•0•Updated Dec 5, 2022Dec 5, 2022

    • SARS_Cov_2_Spike_metals

      Public
      Files for MD simulation of the interaction between SARS-CoV-2 Spike protein and metals
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2022Oct 13, 2022

    • Polystyrene_and_Spike_protein

      Public
      Files for MD simulation of the interaction between SARS-CoV-2 Spike protein and Polystyrene
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • surfactants-coronavirus-CG

      Public
      0•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • Ciprofloxacin

      Public
      For each form of the antibiotic there is: a parameter file with the force field interactions (.inp), a file with the atomic coordinates (.pdb) and a file with the topology data (.psf)
      0•0•0•0•Updated Sep 2, 2022Sep 2, 2022

    • Spike_S1

      Public
      Psf and pdb files for the S1 spike subunit of SARS-CoV-2 virus
      0•0•0•0•Updated Sep 17, 2021Sep 17, 2021

    • sebum_molecules

      Public
      Pdb, psf and parameter files for main three lipid molecules composing the sebum of human skin
      0•0•0•0•Updated Jun 23, 2021Jun 23, 2021