EXIA

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EXIA is the data analysis software package for quantumn mechanics (QM) and molecular dynamics (MD) calculations. This is the portable version. EXIA can be downloaded and placed in anywhere.

• MD Features

MD Features

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• EXIA utilizes features from PYTRAJ to extract the data from MD calcualtions by AMBER including RMSD, bond lengths, angles, PDB extraction, water cluster, and hydrogen bond analysises.
• EXIA has its own feature to extract energy data from MD.

Getting Started

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EXIA can be imported by sys module. It needs output and input directories.

• Examples

import os, sys
sys.path.insert(0, os.path.abspath("../../../../EXIA/EXIA/md"))
import pdb_analysis

system='RE'

traj_name='prod_all.nc'
top_name='RE_solv.prmtop'

for i in range(1,2):
    model=''.join(['model_',str(i)])
    traj_dir = os.path.join('..','..','raw_data','md',system,'result','trajectory',model)
    top_dir   =  os.path.join('..','..','raw_data','md',system,'top_coord',model)
    export_data_dir = os.path.join('..','results','md_analysis_part_1',system,model)
    print('processing on',model)
    pdb_analysis.get_data(i,traj_name,top_name,traj_dir,top_dir,export_data_dir)

Each system has many different substrate orientations which is called as model. system and model are used as the indexs to save the extraced data.

License

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GPL v3.