Post on 27-Dec-2015
transcript
A Project about:A Project about:
Molecular Dynamic Simulation (MDS)Molecular Dynamic Simulation (MDS)
Prepared ByPrepared By
Ahmad Lotfy Abd El-FattahAhmad Lotfy Abd El-FattahGrid Computing GroupGrid Computing Group
SupervisorsSupervisors
Alexandr UzhinskiyAlexandr Uzhinskiy&&
Nikolay KutovskiyNikolay Kutovskiy
Project Description
1- A Molecular Dynamic simulation for a chemical compound is made using the DL_POLY Molecular Simulation Package.
2- Some changes in physical conditions like temperature or pressure are made, after then running the application again to see the changes in the structure of the compound.
3- The same steps are performed again, but using the “Grid”.
Set up and Running DL_POLY software application on Windows
0 - Copy the contents of the software source into some directory.
1- To run the Graphical User Interface (GUI) successfully, it must be started from within the DL_POLY execute subdirectory.
2- Open the Windows command-line prompt and write this command;
java -jar ../java/GUI.jar Note: You need Java VM
The following GUI will open
Input and Output files for DL_POLY Software
Input files Output files
Files marked with an asterisk are non-mandatory
The differences between the input and output data are read from the output file called output , which is a human read file.
Graphically, it is difficult to differentiate between the configurations before and after changing some parameter using DL_POLY (just in our case).
So it is convenient to use another software called VESTA, we used it just to display the input (CONFIG) and output (REVCON) files.
The interface of this software is more user-friendly and easy to control the rotations and views of the configuration.
Running the simulation using the Grid 1- Logging in and initiation of proxy certificate
Command: voms-proxy-init –voms edu
2- Making a new directory and Creating new JDL file
Commands: $ mkdir new_project and : $ vi mdm-openmpi.jdl
Result directory content
We use the WinSCP software to copy the output files from the user interface (UI) to the local machine.
Now we use VESTA to display the input (CONFIG) and output (REVCON) files again to see the new changes.
Acknowledgments
To Alexandr Uzhinskiy for his efforts in practicing us on the grid computing.
To Nikolay Kutovskiy for his guidance and efforts to help me in my project.