Late Breaking news 2012-2013

Offline H drive

The default setup for undergraduates this year is that the desktop and appdata folders are redirected to the H drive. This can cause mystification for laptop users when the machine is offline. Desktop icons vanish. H:\appdata contains settings for Firefox and other programs and things stop working as expected.

To make things a little easier we have enabled caching for the H drive, so it will be available offline. It will synchronise automatically when you are connected to the college network. Do note that it will also synchronise if you are connected via the VPN and if you are on a capped broadband contract you should bear this in mind. - Nick

Firefox, Java and the Wiki

Activating Java 1

Firefox needs Java enabled to run the Jmol applet, which displays molecules, vibrations, MOs etc. The setting which determines this is user specific (it is stored in a file in your H: drive). If you are not getting molecules, but instead a yellow box telling you no Java is enabled, proceed as follows:

In the menus at the top of FireFox, Tools/Add-ons/Plugins.
Scroll down to Java(TM) Platform SE 6 U31 6.0.310.5 and activate it. The security message which indicates that the Java is out of date should be ignored for the time being.
Refresh the Wiki page (or restart the browser). You should get a pop up box which reads The applications digital signature cannot be verified. Run
This indicates that Java is now active again. Run the applet and your molecules should now appear.

Publishing to DSpace

The instructions suggest that you publish select jobs to Dspace. There is current a bug in the profile which prevents this until you have actually activated the publish as shown on the right. Login to the SCAN HPC service and select Profile from the list on the left. Check the button showing Publish to Dspace (it should have been on by default, but in fact its off. Apologies. We hope to fix this shortly).

Also, the publish command needs sometimes to "wake up" the DSpace server. It may not do this the first time you try to publish, but it normally works the second time.
If the job cannot publish, the chances are that there is an error in the job that prevented the writing out of the publication files. You will need to open the job output using Notepad++ (Right-click on the file and select NotePad++ or other text editor such as WordPad) and see what the errors are at the bottom of this file. You may need to discuss these with a demonstrator to determine what went wrong.

Versions of Gaussian

The laptops contain both G03W and G09W 64-bit. Unfortunately, only the first of these is recognised by ChemBio3D V 12. So if you try to run Gaussian from ChemBio3D, it will run G03W. A new release of ChemBio3D V 13 came out over the summer, but try as we might, we cannot get the global licensing codes to reliably work. As an interim measure therefore, we have reverted back to ChemBio3D V12 on your install. However, you can download V13 yourselves for installation on a computer from this site and this will give you a licensing code specific to you which you can use (with only three attempts allowed) to install and license the newer version.

G09W contains many updated features, but you would normally be expected to make use of many of them. Perhaps the only significant difference from your point of view is that you can allocate more memory to run Gaussian using the %mem=2GB command. This should make it run (somewhat) faster.--Rzepa 10:56, 5 October 2012 (BST)

Late Breaking news 2011-2012

Incorporating Orbital surfaces into a Wiki

The procedure is as follows

Run a Gaussian calculation on the SCAN
When complete, select Formatted checkpoint file from the output files and download
Double click on the file to load into Gaussview
Edit/MOs and select (= yellow) your required orbitals.
Visualise and Update to generate them
Results/surfaces/contours and from the cubes available list, select one and Cube actions/save cube
Invoke this page and you will be asked to select your cube file,
followed by three file save dialogs, one for the coordinates (.xyz), one for the MO surface (.jvxl) and a package (.jmol).
Insert the following code into your Wiki, replacing the file name with your own choice from the preceding file save dialogs (the string images/4/42/AHB_mo22.jvxl is for illustrative purposes only and must be edited as described below).

<jmol>
<jmolApplet>
       <title>Orbital</title><color>white</color><size>300</size>
       <script>isosurface color orange purple "images/4/42/AHB_mo22.jvxl" translucent;</script>
       <uploadedFileContents>AHB_mo22.xyz</uploadedFileContents>
     </jmolApplet>
</jmol>

Next, upload the the .xyz and .jvxl files into the Wiki (one file at a time, the multiple file uploader does not seem to work for this task)
1. You will need to find the absolute path for the .jvxl file. Above, this appears as images/4/42/AHB_mo22.jvxl
2. Just after uploading the .jvxl file, you will see a response as shown on the right.
3. Right click on the link (blue arrow) and select Copy file location (this can be browser specific)
Paste this string into the above, and edit it down to just images/4/42/AHB_mo22.jvxl (ie trim https://wiki.ch.ic.ac.uk/wiki/ off if that is how it appears)
You should get something akin to:

Orbital

You can superimpose two surfaces. Change the script contents above to

isosurface color orange purple "images/4/42/AHB_mo22.jvxl" translucent;isosurface append color red blue "images/4/42/AHB_mo23.jvxl" translucent;

The four colours used in this line can be changed to whatever you consider appropriate.

An alternative simpler way of loading surfaces

This method avoids the need to specify paths to files as seen above. Instead it uses the .jmol file (as a zip archive) which contains all necessary information and can be invoked by

<jmolFile text="just a link">AHB_mo22.cub.jmol</jmolFile>

which produces just a link. The disadvantage is that it only supports one surface (you cannot superimpose two orbitals). --Rzepa 07:35, 6 March 2012 (UTC)

Report discussion

A reminder that if your report shows a Blue link (rather than red) at the top, you will find some comments on it, which we make during the marking of the report. This is separate feedback to your grade, which is being processed via the Blackboard system, and may appear a day or so after the discussion. So for instant feedback, look at the discussion.--Rzepa 09:51, 1 February 2012 (UTC)

Crystal structure files as initial 3D coordinates for modelling

The start point for obtaining 3D coordinates can be

ChemDraw via its templates feature, which has a wide selection of small molecules, used as an alternative to sketching the molecule from scratch.
The Corina tool, which can be used to create a Molfile of coordinates from a SMILES string generated using ChemDraw.
The Conquest interface to the Cambridge crystal structure database.
1. Invoke this by typing Conquest into the search box produced by invoking the Windows tool on the bottom left.
2. When a search is completed, invoke export and Mol2 as the format. Select current entry, one file per entry and save (to desktop).
This file should now be readable using ChemBio3D.--Rzepa 12:45, 20 January 2012 (UTC)

Multiple File uploads

At special request, a multi-file upload facility has been added on an experimental basis. The link appears in the sidebar on the left. Please try out and report any problems --Rzepa 13:48, 27 October 2011 (BST)

DSpace depositions

If you have tried to publish a calculation into Dspace recently, it will have failed. This in part is a knock-on effect from the power outage this last weekend, the full implications of which took several days to sort out. As of this instant, publication is working again. If you have something you tried to publish yesterday (Monday) send the portal Job ID to Mat Harvey (m.j.harvey@imperial.ac.uk) and he will correct the entry.--Rzepa 11:25, 18 October 2011 (BST)

Improvements to the Editing interface

An enhanced editing toolbar called WikEd is now installed for all users and most browsers. You should spend a little while exploring its features.

ChemBio3D version 12

Version 12 (and 11) of this program contain several errors/bugs. The vendors were informed of these more than two years ago. Unfortunately, it seems as if V13 of the program will not be released in time to be used on this course. So you will have to watch out for the bugs.

Late Breaking news 2010-2011

Another way of fixing a broken page

Try this method if the revision history method fails. This is based on trying to back up your project (errors and all) to an editable file, and then re-editing the file to remove any error that you manange to spot. --Rzepa 21:35, 24 February 2011 (UTC)

Laptop shutdowns at 22.20

Not too many people are actively using their laptop at 22.30, but what has emerged is that routine maintenance procedures are hard-coded (Crontab) into the software build to reboot the system at this time every day. The maintenance involves applying new security patches, new virus definitions, new software releases etc. If your laptop is online just before 22.30, you may notice this activity. Windows 7 then invariably requires the system to be rebooted for the patches to take effect. This will happen irrespective of whether any software patches have been applied. So, at around 22.15 or so, it is essential that you save all work. If you do not, it may be lost when the system reboots. --Rzepa 13:01, 21 February 2011 (UTC)

Mini Project

During the course of grading the project, I discovered some people did have time to do calculations, but the ran out of time for the write up of the project. If you are in such an unfortunate position, do at least put the DOI of the published calculation into your report (this takes just a few seconds). That way, you can at least get some credit for having selected a molecule and calculated it, even if you do not have time to discuss your results on the project page. As with the Wiki report, the DOI entry is also time stamped, so we can easily verify that the calculation was done before the deadline! --Rzepa 09:32, 1 February 2011 (UTC)

Why Wiki

A question occasionally asked is why the course report uses a Wiki instead of the more familiar (to most people) Microsoft word format. Some of the reasons why are summarised here.

Plagiarism

We have implemented strong plagiarism detectors for submitted reports. This would include detecting similarities with previously submitted reports. You should be reminded that plagiarism is taken very seriously indeed, and any detected will have serious consequences for the plagiariser.

Converters for Wiki

It was there, but it got lost (honestly!). See here for some hints on how to convert other formats (Word, HTML) to the Wiki format.

Prettifying Plots produced by Gaussview.

GV (5.09) can visualise spectra (NMR, IT, etc), as well as SCANs and other properties. However, the resulting graphs are not very suitable for inclusion, since the default text sizes are too small, the lines may be very thin and the units for the labels unhelpful. To tweak these spectra, proceed as follows:

Use Gaussview, and select Results/vibrations or NMR/Scan/UV-Vis etc.
Right mouse click and select properties. Here you can select more sensible units, and also the origin.
Right mouse click and select Export. Save the (.svg) file (SVG is to images what HTML is to text).
Using Wordpad (or other text editor), open up the .svg file
Near the top, you will see e.g. the text Scan of Total Energy. Replace by what you want.
You will see font-size:14; Change to something larger.
Further down, you will see font-size:10; Change to something larger.
You will see lots of stroke-dasharray:3; Delete them all (a global replace).
You will see a line starting polyline. It contains stroke-width:0.9; Change to something like stroke-width:2.7;
You will see a line starting rect. It contains rgb(255,255,245); Change this to rgb(255,255,255);
Save the edits, and drop the .svg file onto a FireFox browser Window. The spectrum should appear. If you make further changes, refresh the browser window to see them.
At this point, you probably want to take a screen-grab of the browser window (as a .gif or .jpg file). Upload this to the wiki to incorporate into your report.

Module 2: VPN for home use

Due to the wiki server being hacked it has been brought in behind the college fire-wall. If you want to access it from home (or the scan servers), you must first connect via VPN. If you don't the wiki will not load.

Module 1: Errors in log file

When running SCAN calculations, if no Checkpoint file is produced, or other errors occur, its best to inspect the Gaussian log file using Wordpad. The errors will be seen at the bottom of this file. However, the default font size for Wordpad is 11, which causes the output in the log file to wrap around, causing it to become unreadable. So before you try to inspect this output, set the font size to 9. This produces much more readable outputs.

Module 1: Iodine containing molecules

Although the Mini project is designed to be based on organic molecules, occasionally other elements creep in. One such is iodine, which causes problems because the 6-31G basis set is not available for it. In such circumstances, you can always go to the basis set exchange to get one. A (partial) example of its use is shown below, in which the built in basis is used for C, but the basis set exchange one for I (in fact the 6-311G basis):

# rb3lyp/gen opt

General basis set, including that for iodine

0 1
 I                 -0.58031145   -1.18849341    0.11015250
 C                  0.73981873    1.76844662   -0.08747886
....

C  H etc   0 
6-31G(d,p)
****
I     0 
S   5   1.00
 444750.0000000              0.0008900        
  66127.0000000              0.0069400        
  14815.0000000              0.0360900        
....
****

Late Breaking news 2009-10

Module 1: Project FAQ

Because the project is defined not in the scripts but by you, it can sometimes seem rather open-ended. So, after an interesting chat with one student, I came up with three possible objectives you could set yourself for the project.

The most ambitious is that you spot a structure in the literature which seems to ring alarm bells. Can it really be that, you ask yourself. Well, if 13C and other spectroscopic data has been reported, you can calculate it and see how well it matches. You might conclude that either its a good match, or not.
A follow up to the first category, is that if the match is poor, you suggest a better one. this is HARD. We do not expect that of you!
More common is that two possible structures have been reported, and you might wish to check that they have been assigned correctly and not transposed.
Another scenario is that the 13C for any given structure is simply reported as a series of values, with no attempt to assign each peak to a specific carbon in the compound. By calculating the spectrum, you can make this assignment.

Any one of the four above is a reasonable objective to set yourself in this project.--Rzepa 15:38, 25 January 2010 (UTC)

Anti-Bredt Natural products?

The blogosphere is buzzing discussing a natural product reported in DOI:10.1016/j.bmcl.2009.10.016 which contains a bridgehead alkene in a small ring. The ¹³C data is difficult to get from the article, but the structure is an interesting one to analyze using the techniques we show you here. Some of the blogs also are commenting on the early modelling efforts A nice breaking news story that you might wish to look at! (the result of all this attention is a corrigendum, DOI: DOI:10.1016/j.bmcl.2010.04.003 ). And how about this (update: This too has been retracted).

NBO of BH₃ has the sAO as the "lone pair"

Something is wrong! The likely problem is that you don't have the ground state lowest energy electronic structure. If you computed the B3LYP/3-21G geometry and then used B3LYP/6-31G to compute the population, the system is not optimised at the B3LYP/6-31G level and your answer will be wrong. Excellent if you noticed this discrepancy. Compute the population analysis and NBO with the 3-21G basis set and you should get a correct analysis. If not, check the energy of your calculation does it give -26.4622632920?

Alternatively if you used the 3-21G basis set ... the new version of G09 prints the NBO analysis slightly differently, the nbo web-page has now been updated to reflect this and explains in detail where to find the correct pz AO.

Could someone perhaps pose the question, to which we see an answer here? --Rzepa 07:32, 20 January 2010 (UTC)

Displaying Vibrations

The write-up section of the course describes how you might animate a vibration using the Wiki. Unfortunately, our upgrade to Gaussian 09 brings with it changes to the manner in which the vibrational information is written out, which Jmol cannot understand. The result is an error message rather than a vibration. I have contact Bob Hanson, editor-in-chief of Jmol and no doubt a fix will be sorted out shortly. --Rzepa 13:09, 16 November 2009 (UTC)

UPDATE: The problem noted above is now fixed. If you take a look at this entry you will see Jmol reading a Gaussian 09 vibration log file and displaying a vibration. This new version of Jmol offers other new features. If you right-mouse-click, a menu appears. The top item of this is the data model. This will contain all the optimisation steps in the log file, together with all the vibrational modes identified. Any one of these can be selected for display.--Rzepa 08:30, 17 November 2009 (UTC)

Backing up your report

Invoke this utility to back your project up. In the box provided, enter e.g. Mod:wzyz1234 being the password for your report. This will generate a page (right) which can be saved using the Firefox File/Save_Page_as menu. Specify Web Page, XML only as the format, and add .xml to the file suffix. You might want to do this eg on a daily basis to secure against corruption. This is in addition to the notes for how to repair broken pages.

The same file can now be reloaded using Import.

Using the LANL2DZ Pseudopotential Basis set

We have reports that using the keyword b3lyp/lanl2dz for elements such as Al and Cl produces an error-free log file, but no .fchk file is produced. This is because the conversion program that converts the initially produced .chk file to .fchk (a process needed because the .chk file is specific to the type of computer the calculation was run on, and will not work on Windows computers) is failing to covert the file. We think this is probably an error in the way Gaussian09 produces that .chk file rather than a failure of the converter (the error has been reported to Gaussian for clarification).

One option is to take the optimised geometry and carry out a single point calculation with a full basis set, for example 6-31G(d) which is the same as 6-31G* (just different notation) and then use the checkpoint from this job to visualise the MOs.

Another alternative is to use the following keywords: b3lyp/Gen read=pseudo and then after the blank line that terminates the geometry, to read in the basis set and pseudopotential. These can be obtained from the Basis set exchange. Select all the elements present in your molecule from the Periodic table display, and from the left, select the Orbitals with effective core potential pull down. Then scroll to LANL2DZ ECP, select as the format Gaussian94 and press Get basis set. A Window appears, and you should select all the content in that Window and paste it into your Job input file (using eg Wordpad) after the geometry blank line. One further edit is needed. The section in the basis starting

! Elements ...

is terminated by two blank lines. Delete one of these blank lines (leave the other). The result should look something like this (only Al is shown in part, the other elements are not shown for brevity).

 H                  3.33099000   -2.03083200   -0.89612200
 H                  1.96515000   -2.65853800    0.03207800

Al     0 
S   2   1.00
      0.9615000             -0.5021546        
      0.1819000              1.2342547        
S   1   1.00
      0.0657000              1.0000000        
P   2   1.00
      1.9280000             -0.0712584        
      0.2013000              1.0162966        
P   1   1.00
      0.0580000              1.0000000        
****
! Elements                             References
! --------                             ----------
! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
!          P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
!          P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).
!   

AL     0
AL-ECP     2     10
d   potential
  5
1    304.7291926            -10.0000000        
2     61.5299768            -63.8079837

The advantage of the general basis set is that a very much wider selection of basis sets is available (Gaussian only has a sub-set of these built in), including many of the most modern.--Rzepa 09:40, 30 October 2009 (UTC)

Slow Running of laptops

We have had some reports of slow response using Gaussview. This has been identified as having too many programs open simultaneously. This is a generic problem, which we suspect most people experience at some stage in their use of computers. It does not appear to be connected to this lab course in particular. Before you conclude your laptop is malfunctioning, try closing down all the programs except Gaussview and see if it makes a difference.

Associating FireFox with Gaussview 5 not 3

Gausview 5 was received very late by us (late September 2009), and has not been subjected to full testing. We installed it for compatibility with Gaussian 09, and some properties (Vibrations) need GV5 to display properly. Currently, when FireFox is used to inspect Gaussian 09 computed vibrations, it starts up GV3 rather than 5. To reconfigure the browser for GV5, proceed as follows:

In the Tools/Options menu, select Applications
Find the entry for OUT file and Click on the associated action
Set it to always ask
Now a prompt appears on downloading a Logfile, so browse to gauss.exe (in Program files/GV5) and check do this automatically from now on.
This should ensure that GV5 rather than GV3 is invoked automatically.

Queue status

Some people have queried how the queues work. Below is a brief explanation made to those students in an email. It might help you understand what is going on under the hood.

The queues do seem normal in most respects. As of 16.00 there were 16 jobs running in chemlab1 (the max) and 19 pending. By about 20.00 the number of pending jobs were down to 3. This morning at 07.00, only 3 jobs remained in the queues, none pending. This is pretty much what one expects. Chemlab2 on the other hand has all machines still claimed as of this morning. I am checking out if this is simply a full queue, or a hung queue! If the job on this queue does not complete by 7.30, it is stopped (so that the machines can boot back to windows) and an attempt to run it again next night is made. If the job cannot complete in 10 hours (because the molecule is big, ie more than about 20 nonhydrogen atoms), it will only run to completion on weekends, or on chemlab1. This is why the instructions suggest using maxcycles=25 (or less). This limits the job and allows it to complete overnight.

Very much part of this lab is learning to manage your resources. It might be a steep learning curve, but it is also very much what the real research world is about! Fortunately, Moore's law does mean that you get more bang for buck each year. Thus for both vibrations and 13C, Gaussian 09 is about twice as fast as what we had last year! But do remember that the time scales as N**4 (N= number of atoms). So only a few methyl groups extra can double the calculation time!

If individual jobs fail with no output, this probably indicates either a problem with an individual user's account (Matt Harvey will tell us), or that the input is too defective to produce any. In this latter category, do spread the word to come to my office and I will perform a triage on this before escalating to Matt. --Rzepa 07:20, 22 October 2009 (BST)

Remote connections and use of Gaussview on non College Computers

RDC connection

With laptop hand-back not fully overlapping with write-up deadlines, a number of people have asked how they might be able to access the course programs without the need to physically be present in the two computer rooms. The Gaussview license in particular does not allow installation on non-Imperial computers. To overcome this restriction, you can do the following:

Use Remote Desktop Connection, which is installed on most Windows computers.
Establish a VPN connection if you are off-campus
Connect to chas.ch.ic.ac.uk (the chemistry application server). You will be presented with the same screen as you would if you were physically at the computer. This includes all the software etc.
You will find that some operations are more stodgy than others (surface rendering for example) but if you have a reasonably fast (i.e. broadband) connection, the experience is not too bad.##You can test the above (but without the need to set up the VPN) from one of the static computers in the computer rooms.--Rzepa 12:55, 18 December 2008 (UTC)

Conversion of Word to Wiki format

If you prefer to author your report using Word, and then at the final stage convert it to the Wiki, you can do so using OpenOffice 3.0. This has a Word to MediaWiki converter which allows you to save the file in Wiki text. This can then simply be pasted into your Wiki page. It might need some tidying up (in particular, Jmol molecules can only be added at the wiki stage, and not so in Word itself), and you will have to still upload the graphics in the Wiki. Since Januar 2009, V 3.0 of openoffice has been installed which supports this feature.--Rzepa 17:05, 23 January 2009 (UTC)

Several people have reported that Word is crashing during use. We think it might be because you have used it to open a document located on the network drive H:. If your network goes down (see above) whilst you are editing the document, Word may well panic and hence crash! To avoid this, and whilst you still have a network, make a copy of any Word document from drive H: to the hard drive E:. Then, only ever edit that local copy. Finally, when you are finished, copy the document back from E: to H:. Hopefully, this will avoid any Word crashes.--Rzepa 10:37, 17 October 2008 (BST)

Email Alerts

You can receive email alerts if any page on the wiki is changed (ie when additions to this page are made). Click on the watch link at the top of any page and then on the my preferences link (you have to be logged in), tick the E-mail me when a page I'm watching is changed box.

Mod:latebreak

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