dimerizer module
The package containing the i/o functionalities required by the dimerizer script.
Dimerizer can deal with the following files:
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pdb
The configuration of the system provided in pdb format. This file is read and the specified part of the system will be dimerized.
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topology
The Gromacs topology file describing the bonded and pair interactions between atoms.
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mdp
The Gromacs settings .mdp file. Some options have to be activated/deactivated in order to set up a Dimer simulation.
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index
Different energy groups are declared in the .mdp file and the relative index files are created here.
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plumed
The Plumed plugin is required for Metadynamics and to introduce the Dimer interaction in the system. A minimalistic file can be created with this package.
""" The package containing the i/o functionalities required by the dimerizer script. Dimerizer can deal with the following files: * # pdb The configuration of the system provided in pdb format. This file is read and the specified part of the system will be dimerized. * # topology The Gromacs topology file describing the bonded and pair interactions between atoms. * # mdp The Gromacs settings .mdp file. Some options have to be activated/deactivated in order to set up a Dimer simulation. * # index Different energy groups are declared in the .mdp file and the relative index files are created here. * # plumed The Plumed plugin is required for Metadynamics and to introduce the Dimer interaction in the system. A minimalistic file can be created with this package. """
Sub-modules
Utilities necessary to modify a forcefield by adding the required interaction terms.
Creates a Gromacs index file.
In Gromacs non-bonded interactions can be computed specifically for subsets of atoms and for each subset the shape of the interactions can be provided with a table. In the index file the atoms belonging to each energy group are specified. The format is simple: -----...
Edits the Gromacs .mdp file.
A Gromacs .mdp file contains various informations about the simulation setup ranging from the Molecular Dynamics timestep to the thermostat parameters, output management and so on. A Dimer simulation in Gromacs requires some of these settings to be set in a particula...
This module contains the functions required for the optimization of the replicas: given a defined number of replicas, optimization means producing sigma-parameters that give a sequence of replicas with an exchange probability of roughly the target value.
The optimization is made for a collectio...
This package parses, modifies and writes pdb files
The standard Gromacs .pdb input file is mandatory and this package produces a dimerized version of the file. Dimerized version means that each non-solvent atom appears as a structure consisting of two beads and one (optional but suggested) virtu...
A collection of plumed inputs for a minimalistic Dimer simulation.
Plumed is used here to introduce the Dimer interaction in Gromacs.
This is obtained with a linear restraint on the Dimer collective variable (CV). The Dimer CV is the binding energy of the Dimer and should be available in a future...
Modules that parse, modify and write topology files
Topology files are built starting from a standard Gromacs .top file given as input. There are basically three operations to be made on the input .top file:
- The [ atoms ] section has to be extended to take in the new atoms added in the .pdb file...