Objective: This assignment is designed to introduce you to running a simple dynamic molecular model and transfering your results onto a UNIX workstation. by using ftp.
In this assignment you will learn how to:
Your grade will be based on creating the following files in your own personal directory so that I can reproduce your results by going into your directory and accessing your files. You can work together as a team on this project however I expect everyone to generate your own files. The files I expect to see in your directory are:
INSTRUCTIONS:
A molecular dynamic procedure that is already outlined in some detail in the topics section of the MSE2094 Class Notebook assumes a working knowledge of UNIX. Assignment#8 only requires that you know how to login and transfer files to the UNIX workstations in the sciviz lab in 202A Hancock. The next assignment (#9) there is a more extensive procedure listed Assignment 9 that will supplement the procedure already listed below.
For this assignment you are only required to download correct a few typical compile errors and generate an output file of results. To grade your results I want each student seperately to transfer their three files (molec_dyn.f, md3.in, md.out) onto viz2.sv.vt.edu UNIX workstation.
1. Logon to your account on planet-name.smvc.vt.edu
Either go into the sciviz lab (Hancock 202A) or login remotely to planet-name.smvc.vt.edu
First create a directory named assign#8 by using the UNIX command "mkdir assign#8". Verify this directory has been created with the UNIX command "ls -lag" which lists all files and directories. Next change directories by using the UNIX command "cd assign#8" which gets you into the assign#8 directory. List the contents of this directory by using the UNIX command "ls -lag" again and you will see that this directory is empty. To check your position in the directory tree structure use the UNIX command pwd (p-rint w-orking d-irectory) and the path to your directory will be listed, e.g. /home/username/assign#8. Your assignment is to create the files already mentioned above and transfer these three files into the assign#8 directory.
2. Use Netscape or equivalent web browser to download files: md3.in and molec_d.f
You can start at the sciviz home page (http://www.sv.vt.edu) if you wish and select the following sequence to get to the Molecular Dynamics Exercise: Courseware Development, MSE2094, additonal information, Molecular Dynamics and the web page on Understanding Molecualr Dynamics will appear. Scroll down to the flashing Molecular Dynamics Exercise section and you should see five hypertext files:
3. Download files and get the Fortran program working
Down load copies of two of these files (molec_dyn.f and md3.in (inside Sample Inputs)) onto your PC, for example select molec-dyn.f and you will see a copy of the Fortran program. With the left mouse button under "File" choose "save as" and a new window should appear. In this window with the left mouse button select the appropriate directory name to store these files. Similarly download md3.in. Notice when you select Sample Inputs you have a choice, select the file named "md3.in" the same as you did with the "molec-dyn.f file". Before we can use these files a few modifications must be made.
NOTE: if you prefer you can do everything on the UNIX workstation without having to download the files from the web onto your PC and then modifying the fortran programs on the PC. If you do everything on the UNIX workstation, create a README file in your assign#8 directory explaining what you did (EXTRA 50 pnts).
Using a text editor remove the first five lines of the molec_dyn.f program which are html hypertext lines. After the five lines have been removed go down about 20 lines to the statement OPEN(UNIT=2, FILE='md.in') and change md.in to md3.in .
3. ftp files onto your account on the UNIX workstations:
Part I (200 pnts) Deliverables.
http://www.eng.vt.edu/eng/materials/classes/MSE2094_NoteBook/HomeWork/assign8.html