06-640: Molecular Simulations

Accessing Andrew Unix Workstations from Windows NT Machines

This document provides an overview of several pieces of software that can be used to access the Andrew Unix machines from a PC running Windows NT. Access to these Unix machines will needed to use MATLAB and also to run some of the case studies from our textbook. All the software described below is installed on the PCs in the computing cluster located in Baker Hall 140C. Note that there are multiple ways to perform almost all of the tasks described below. This document outlines one specific means of access. If you prefer to use variations on these tools, for example a different telnet or ftp program, you are of course welcome to do so. If you prefer to use another computing environment you may need to adapt some of the directions below.

You should not hesitate to contact Prof. Sholl if you are having trouble with computer access, finding the right software etc. The aim of this class is to learn about molecular simulation techniques, and we dont want computer difficulties to obstruct this goal. If you discover any inaccuracies in this document, please let us know so we can update it.

Throughout this document, anything that you need to type on the computer is shown in courier font.

Logging In and Opening Windows

UNIX workstations use an interface called X-Windows to open multiple windows simultaneously. The instructions below describe how to access this interface from a PC.

  1. Login in to the PC using your andrew login and password.
  2. Set up the PC to allow emulation of X-windows by clicking on the Start button and following this sequence through the pop-up menus:

Start Programs Communications X-Win32 X-Win32

A box should appear on the task bar at the bottom of the screen saying X-Win32.

  1. Connect to the UNIX machine using telnet by clicking on

Start Programs Communications Nifty Telnet Nifty Telnet 1.1

In the telnet window that appears, enter unix.andrew.cmu.edu as the Hostname and then click on Connect. You will be prompted for a login and password.

  1. You must give the UNIX machine permission to display windows on your PC. To do this, type setenv DISPLAY pcname:0 at the UNIX prompt, where pcname is the full name of your PC. A typical PC name in Baker 140C is banzai.bh.andrew.cmu.edu .
  2. Now you can open up one (or many) X-windows. To open a standard terminal window, type xterm & at the prompt in the telnet window. The "&" sign tells the computer to execute the command while retaining access to the prompt in the window you type the command. If you forget the "&" sign, an X-window will open, but you will no longer be able to use your telnet window until you close the X-window.
  3. You can open up as many X-windows as you like by typing xterm & repeatedly in your telnet window. Try it. This is useful because you frequently want to have access to multiple windows to edit an input file, run a program, look at output and so on.
  4. Once logged into the UNIX machine, you can use any of its features in any of the windows you have open. For example, you can read and send email using pine .

Logging Out

To logout when you have finished your work, follow these steps:

  1. Type exit at the UNIX prompt in each of the X-windows you have open. You may have to quit whatever program you have been using in that window before doing this.
  2. Type exit or logout at the prompt in the telnet window.
  3. Logout of the PC by clicking on the Start button and going to Shutdown on the pop-up menu. In Baker Hall, select the Log Out and Log Back In As Another User option.

Ive Logged In - Now What?

To run MATLAB, simply type matlab at a UNIX prompt. More information about MATLAB will be given in a separate document.

To edit a text file, a number of screen editors are available. One that is simple to use is pico, the editor that is used by default by the email program pine. Type pico at a UNIX prompt and use the commands listed at the bottom of the screen ("^X" means control-X and so on). Other editors that are available include vi and emacs.

To plot data, it is easiest to copy the data file from the UNIX machine to your PC and then use Excel or another graphics package to make the plot. To move files between the two machines, use FTP by clicking on the PCs Start button and following this set of pop-up menus:

            Start Programs Communications WS_FTP LE

In the FTP window, enter unix.andrew.cmu.edu as the Host-name. You will be prompted for your login and password.