Bash Script to perform Umbrella Sampling Simulation on Alanine dipeptide in vacuum.

• Authour:

    Anji Babu Kapakayala
    C/O Prof. Nisanth N. Nair
    Dept. of Chemistry
    IIT Kanpur, India.
  

• USAGE:

    sh Umbrella_Sampling_setup.sh
  

• Requirements:

    Plumed and Gromacs should be installed with mpi
    gfortran, gnuplot, mpif90
  

• INPUTS:

    ala_di-pep.gro and ala_di-pep.top
  

• Description:

    This script will generate required input files and run the umbrella sampling simulation
    for alanine dipeptide in vacuum using gromacs and plumed (optional) for 2 ns. And constructs 
    the 2D free energy along Phi and Psi collective variables
  

• Directories:

  On the fly, It will create following directories and stores related files in those directories:
               
        * MIN       : write necessary input files and does the energy minimization.
        * NVT       : Writes the required input files and performs equilibration here.
        * US        : Performs the USa Simulations here in respective directory for every CV value
        * US/INPUTS : Stores all required input files here        
        * US/ANALYSIS: Writes all required inputs here to do analysis 
        * US/PROB   : Stores all the  probabilities corresponding to all the umbrella windows here
        * US/WHAM   : Performs WHAM run here 
  
  
  
        Cheers !!
       Anji Babu