cgmm_model CGMM
Coarse Grained Molecular Mechanics forcefield for protein dynamics		 iisc_logo

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CGMM forcefield has been implemented in GROMACS-4.5.5 software package using tabulated potential form. You have to install GROMACS in your local machine for using CGMM forcefield. Please download GROMACS-4.5.5 and install it. You may use later versions of GROMACS as well; however, we have not specifically tested CGMM and the associated scripts in these versions.
  • Download GROMACS-4.5.5
  • Installation instruction of GROMACS-4.5.5

    • .itp and .gro file:
    For .itp, .gro and .top file of a particular protein please download "itp_gro_file_creator.zip" file and keep your pdb file (XXXX.pdb) in the new directory created from the downloaded file.
  • Please go through the tutorial to know how to create all GROMACS input files.
  • Please go through tutorial for creating topology files (.itp, .top) and coordinate file (.gro) for GROMACS software package.
  • Download cgmm.itp file. The file has atom description of the CGMM forcefield. (metal atoms are also included)

    • .mdp file:
    Simulation parameter input files are:
  • emcg.mdp   (Energy Minimization);   eqpr.mdp   (Equilibriation Step);   rn002_1micro.mdp   (1μs long MD Simulation).
    • Simulation parameter input files for metallo proteins are:
  • emcg_metal.mdp   (Energy Minimization);   eqpr_metal.mdp   (Equilibriation Step);   rn002_1micro_metal.mdp   (1μs long MD Simulation).

    • Potential energy function in tabulated form :    table.tar.gz
    Potential energy function for metalloprotein in tabulated form :    table_metal.tar.gz
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