Using Molden to view a geometry optimisation

Using Molden to view a geometry optimisation

• Modelling programs which run in PCs let you see to some extent what they are doing during a geometry optimisation
• The programs Gaussian and Gaussview provide extensive facilities for modelling, particularly by electronic methods
• They can be bought for a PC, but they are expensive
• We have a copy of Gaussian on a University unix machine which any of us can use at no further cost
• We have not currently bought Gaussview for unix, to set up and view the progress of jobs, but this can be done using the free software Molden
• Molden is already set up on the unix machines:  you do not need to install it yourself
• To use Gaussian or Molden you need a UCS unix id, which will be obtained for you  if you do not have one already
• You need to set up software to use unix from a Cluster PC, as described in BWT's Using Unix from a Cluster PC running Exceed
• The instructions in this tutorial assume that you have set up your unix id to use BWT's own commands
• Sign on to unix and open at least one xterm window by giving the command

xterm &
(This means 'set up a new X terminal session in the background'.  The & after a command means 'do it in the background'.  If you left out the &, the new session would start in the current window, which gets you no further forward;  by giving the &, you can go on using the original window as well.)
• In unix, upper case letters and lower case letters have different meanings.  For almost all purposes, use only lower case, otherwise your commands will not be recognised
• To try out molden, proceed as follows
• cd    ~nbwt3/work/listen
• This changes directory to a BWT directory where some files for this course are stored temporarily.  (In unix, it is easy to permit people to read files and directories, without letting them write there.)
• Remember that when you are using eXceed on a PC to work in aidan, you are actually using the same or a very similar computer to work with the files, as I did when I set them up from my office PC.  Your PC is only used to see what is happening, and control it.  This is quite different from networking PCs, when it is your PC that actually does the work.  You can do exactly what I can, the only difference being that I can write to my unix filespace and not yours, and you vice-versa.
• Give the BWT command

dir
• This lists the files in this directory
• (The standard unix command for this is

ls -la
)
• You will see that there is a file called

p3bu3si2pm3.log
This is the output from a Gaussian geometry optimisation of (Me₃Si)P(Bu^t)P(Bu^t)P(Bu^t)(SiMe₃) which was the first model shown in the course.  As you can see, the actual calculation was done on the 25th September 2001:  you are just going to use molden to interpret what has already happened.  Serious modelling calculations are often done unattended, and you look at what happened afterwards.
• Give the BWT command

molden
• A black molden window opens (it is using your eXceed server without you telling it to)
• A blue molden control window full of buttons also opens
• In this, press the Read button
• You will see a listing of the directory from which you invoked molden
• Single click on the name of the log file p3bu3si2pm3.log
• There is a delay, while all of the long file is read
• After some pinging, which is molden tut tutting because I have not designed the run specially to its needs, you will see the message First point in a box at the bottom of the control window
• Switch off the Molden File Select window by pressing its Close button
• You now see a picture of the starting molecule as a stick display
• Press Solid, Ball & Stick
• You can make the picture beautiful by pressing Shade, but this will make manipulations inconveniently slow on older PCs.  These buttons are flip-flops:  you switch them off by pressing them again.
• For easiest manipulation, click the black dot in the bottom right hand corner of the control window.  Molden pings happily. This allows you to rotate the molecule by left dragging.  Try it.
• View the geometry optimisation by pressing the Movie button
• There are 68 atoms, so the geometry optimisation was minimising the energy in 198-dimensional space.  This is not readily conceived, nor the movements understood, by a human being.  However, Gaussian got it right, because the energy converged, as we shall see later
• To examine the table of bond lengths and angles (the 'Z-matrix') press ZMAT Editor
• A Z matrix is easy to understand, but a bit difficult to invent by hand, though, for very symmetrical molecules, this is sometimes the easiest way.  Fortunately, molden does a very good job of inventing it for us, starting from xyz coordinates from a modelling program.  Here, you just need to understand the structure.
• Line 2 tells you that atom number 2 is phosphorus, separated  from atom 1 by the distance in the second brown column
• Line 3 tells you that atom number 3 is phosphorus, separated from atom number 2 by a distance in the second brown column, and at an angle at atom 2 to atom 1, shown in the third brown column
• Line 4 tells you that atom number 4 is carbon, at a certain distance from atom 2, where it subtends a certain angle to atom 3.  The fourth brown column is the torsion angle 4-2-3-1
• And so on.  Try clicking on the bond angle for atom 4.  You will see the atoms involved in the angle lit up.
• Click on the title bar of the molden molecule window to bring it to the front, and you will see that the same colour rings have been put round the atoms involved in the angle, to make it easy to find out where is where in the Z matrix.  You can rotate the molecule complete with the rings to make it easier to see.
• Click on a different atom in the ball and stick picture, to change the highlight.  You can get the control window, and here the ZMAT window, by right clicking in the model window.  Click on the title bar of the Z matrix window.  You will now see that the selected atom is highlighted in the Z matrix.
• If you move the mouse cursor (do not press the buttons) off the bottom of the Z matrix window, eXceed will automatically scroll the window up your screen, so that you can see the rest of it.  You can see that molden offers quite a lot of facilities for tinkering with the Z matrix, to build related molecules without letting a modelling program alter any dimensions that you want to keep as a new starting point for a geometry calculation.  For use in research, you can read about this on the molden website, or BWT may be able to advise.
• In the control window, press the First button.  The Z matrix of the starting geometry appears
• Press Movie, then immediately the title bar of the Z matrix window:  you will see all the distances and angles changing simultaneously, as the geometry optimisation proceeded
• Next, look at what happened to the energy:  switch off the Z matrix window by pressing the ZMAT editor window on the control panel.  Now press 'geom. conv.'
• You see three graphs, each against points in the optimisation process
• The first is energy, which you can see coming down steadily in this calculation, except for one major blip where the minimisation routine missed its target
• If you click on this point in the graph, the corresponding point in all three graphs is ringed (and, in due course, the corresponding geometry is shown in the model window)
• You can see that the step graph has just taken a big step, because the minimisation routine could see into a new minimum, which is why it missed.  On the force graph you can see that there is now a big force to go down into the new hole.  This process is repeated on a smaller scale on a couple of further occasions, before the molecule settles into its final conformation.
• To exit from molden, press the skull and crossbones button, and answer OK
• To exit from your x windows, type exit
• To exit from the Secure Shell Client signon to unix, type exit, then close the window
• Press the big red button of the X server control panel, and tell it OK