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dimerizer module

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.

"""
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

dimerizer.forcefield

Utilities necessary to modify a forcefield by adding the required interaction terms.

dimerizer.index

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: -----...

dimerizer.mdp

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...

dimerizer.opt

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...

dimerizer.pdb

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...

dimerizer.plumed

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...

dimerizer.topology

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...