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

The software needs input and output files

Input and Output files for DL_POLY Software

Input files Output files

Files marked with an asterisk are non-mandatory

Different minus to construct and set properties for a simulation

Running the simulation

Changing some physical properties like temperature and pressure

and running simulation again

The result after changing temperature and pressure

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

Final JDL file

Shell files:

3- Submitting the job

command:$ glite-wms-job-submit –a mdm-openmpi.jdl

4-Checking Status: Scheduled – Running – Done

command:$ glite-wms-job-status <job ID>

5-Getting the output

command:$ glite-wms-job-output –dir <dir.> <job ID>

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.

Thank You