Metadata-Version: 1.1
Name: dimerizer
Version: 1.0.1
Summary: The dimerizer script for Dimer simulations in Gromacs
Home-page: http://github.com/marckn/dimerizer
Author: Marco Nava
Author-email: mark.nava@gmail.com
License: GPL
Description: # dimerizer
        ---
        This is a tool to convert a standard Gromacs input to a dimerized one. 
        [Gromacs](http://www.gromacs.org/) is a popular tool for proteins simulation.
        This script allows to run Gromacs simulations with [Dimer Metadynamics](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00691), 
        a replica exchange method recently introduced to enhance the sampling of a probability distribution.
        This scripts takes a standard Gromacs input, that consists of:  
        * A simulation settings file (.mdp)
        * An initial configuration file (.pdb)
        * A topology file (.top)
        * A forcefield folder, here we have tested charmm22* and charmm36 but any charmm forcefield *should* work.  
        
        The result are modified files for the dimer replicas. See the examples folder for a quickstart, and 
        the doc folder for the inner workings of the script. A paper will be shortly published to explain in details 
        how this is done and show some benchmark and new tests of Dimer Metadynamics.
        
        
        This is a python2.7 code, to install it remember to use the correct pip version (i.e. pip2.7).
        
        # Auxiliary scripts
        
        There are also two support scripts that help setting up and controlling 
        the simulation. 
        
        ## plread
        
        plread scans through plumed.*.dat files in search for the keyword given as 
        argument and then allows to edit the value in each of the file with a single command.
        
        ## tune_replicas
        
        tune_replicas is a script that given the parameters of the first replica will create a number 
        of replicas with parameters so that the exchange probabilities are close to the target value.
        
Keywords: protein simulation dimer gromacs forcefield
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
