Download Molecular Dynamics Simulation Program MARBLE User`s Manual

3.Tutorials
3. Tutorials
3.1. Calculation flow
MARBLE carries out molecular simulations with the following calculation processes.
The user is first required to prepare structural data of the target molecule in PDB format files (i.e. the files
in the format for structural data in the Protein Data Bank, hereafter called "pdb files").
3.1.1. Executing the molx
Usage: molx input_file
Using the molx, construct the desired simulation system for the target molecule, and generate data files
containing structural data, force field parameters, etc., necessary for the MARBLE calculation.
The molx executes the following procedure based on the pdb file of the target molecule:
 Adds hydrogen atoms and chemical modifications (e.g. disulfide bonds, etc.), on target molecule
(model building)
 Constructs the molecular simulation system by defining a periodic boundary box and adding water
molecules, ions, etc. (system building)
MARBLE calculation flow
3.1.2. Files generated in the molx
The molx generates the following files containing the data of the constructed simulation system.
pdb file
This is the pdb format file of the entire constructed system.
crd file
This file contains the coordinate data of the entire constructed system. MARBLE performs calculations
using the coordinate data in this file.
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