Monthly Archives: August 2010
I usually read the whole info on the Statistics page that WordPress provides to this blog in order to know how many visitors drop by during the week; what other sites are sending me some traffic, if any, or what searches are readers performing which leads them to my blog. Last week I found this post title as one of the Google searches that ultimately made someone find my blog. Of course the combination of the words “theoretical” and “chemists” is what made this blog appear in the results since that is the main topic of it. I found it very curious and funny so I decided to write about it.
I found it funny because this means there is someone worried about making a career choice that might not be the most beneficial in economical terms. I understand the searcher was probably playing and didn’t really mean to find some information about how much do we make but maybe he or her also thought it was worth the shot. Now for the answer to this day’s topic: We don’t do bad at all! It’s true! A chemist, a researcher, any scientist, has a strong motivation towards doing academic research in which it is widely known that not too much money is available if you compare it with the earnings of an MBA working at a big corporation. However a more than decent lifestyle is quite achievable. Of course it varies from one country to another and from one institution to the next, but in more or less developed countries a comfortable lifestyle is the norm. If you are attracted to theoretical chemistry and you have strong computational skills as well as an inclination towards solving problems and not only just posing them, then you can make a lot of money; and I do mean a LOT! Chemical companies are becoming aware of the benefits of having simulations run over their processes at various levels. They realize this is a cost effective as well as an environmentally friendly approach. Software companies which develop all the programs I use on a daily basis need not only people who can program but who also understand the underlying physicochemical and mathematical principles behind each calculation. Pharmaceutical companies have exploited computational chemistry to the point where it has become a standard tool in their research and product development (QSAR for instance). Having worked on both sides now (private and academic research) I can tell you there are as many opportunities of making money in computational chemistry as in any other branch of science but sometimes you have to convince people that what you do is important and valuable. This is called “selling”; only that you are not selling a product, you are selling your ideas for posing new thought schemes or your skills to solve ongoing problems.
As any other job being a computational or theoretical chemist has its caveats; for instance in academics salaries are lower than they are in the industry and finding sources of funding can be a rather time consuming task, not to mention all the bureaucracy you have to endure the entire time. Doing research for a private company has no problems finding funds, resources are available in short time, there is less bureaucracy but in exchange for all that you have to sell your projects to the company, making them attractive for them to fund or you wont have a green light; your creativity has to be oriented towards the company needs, which is not bad at all! There are many challenges in industry as well as in academics.
And as in any other job, through effort comes excellence and through excellence come success and rewards; whether economical or otherwise. If you want to be a computational chemist and drive a Porsche, you can do it! you just have to push yourself to be the best so you can have an opportunity at the best academic or industrial facilities in which at some point your skills will become appreciated and rewarded.
Now, for the closing thought. To young students out there: I cannot stress enough how important it is to work on something that captivates your passion and imagination -whether you get paid a little or a lot- because you have to wake up every single day of the next fifty years of your life to do it for most of the duration of each day! No salary can compensate the opposite, trust me.
Teaching has never been my cup of tea. Karl Friederich Gauss said “Good students do not need a teacher and bad students, well, why do they want one?” I once read this quote somewhere, and although I don’t know if he actually said it or not, there is some truth to it. It is known that Gauss didn’t like teaching, still spent most of his life doing it. Anyway, teaching is important and it has to be done!
Therefore as part of my duties as researcher at CCIQS I will have to teach a class at the Faculty of Chemistry of the Mexico State’s Autonomous University (UAEMex). Obviously they want you to teach a class on a subject you are an expert on; I could teach organic chemistry for sure, despite the fact that I haven’t touched a flask in years. My colleague, Dr. Fernando Cortés-Guzmán and I seem to be two of the very few theoretical chemists around so it is up to us to teach all classes within the range of theoretical chemistry, computational chemistry and their applications. This year someone, I still need to find out who, came up with the idea that an interesting application would be QSAR which of course is a very relevant model for drug discovery. Thus, starting today, I will be the first teacher of this subject at UAEMex’s Chemistry Faculty. Although to be quite frank, I think I would have felt better teaching calculus or differential equations, since those already have a syllabus. On the other hand, those subject wouldn’t get me in touch with students in their final years who are the ones to be attracted as potential students for my incipient research group. It has been interesting so far, building the syllabus from scratch; finding all the topics that are worth covering in a semester as well as a proper way to illustrate and teach them. It will be a work in progress all the time and I intend to expand it somehow beyond the classroom; my first thought was to record all the lessons for a podcast. I’m still not sure how to include this blog into the equation or if I should open a new one for the class but I guess I’ll figure it out along the way. I’m not an expert on QSAR or QSPR but I know a good deal about it, mostly because of Dr. Dragos Horvath whom I met in Romania years ago. Perhaps I could persuade him of leaving Strasbourg for a couple of weeks and giving a few lectures.
Wish me luck, or maybe I should say: “wish my students luck”!
This post will become updated continuously in order to include as much of these useful tips as I find along the way, so if you are interested please subscribe so you don’t have to visit often. Some are old or even a bit obsolete in terms of software versions but I still include them so they can all be gathered in one place; this is basically a summary of some common errors in the use of Gaussian (G03 and G09). Please feel free to comment on this post, sharing your tricks with various programs in whatever branch of computational chemistry you might be working on.
Vibrations calculated with Gaussian 09 can’t be visualized with GaussView 3.x
*Change the lines “Atom AN” with “Atom AN”. They look the same but there are TWO spaces in the first (this is the way G09 prints the output files) and in the second one there is only ONE space. The credit is entirely due to Jean Poully who posted this trick on the CCL a few months ago.
*Reader John Keller from Alaska suggests to use the formatted chk file (.fchk) to avoid this problem. As usual with formatted chk files make sure you format them in the same computer where you calculated it, or at least make sure both versions are compiled under the same architecture (32 or 64 bits).
Molecules appear flat on Molekel versions previous to 5.x
Molekel 4.x reads Gaussian98 files only. Gaussian03 and Gaussian09 files need to have the header corrected in the following part, right at the beginning of the file:
Gaussian 09: EM64L-G09RevA.02 11-Jun-2009
Gaussian 98: EM64L-G09RevA.02 11-Jun-2009
A rather old one and kind of a weird one too but it works and some of us (myself very much included) like the previous Molekel far more than the new 5.x version.
Electrostatic potentials can not be visualized with Molekel 4.x
This is an error that stems from the fact that atomic charges are not read by Molekel, so all electrostatic properties derived from them are not calculated nor visualized. The problem is that Gaussian also changed the header for the charges when going from Gaussian98 to Gaussian03. In Gaussian 98 charges are labeled as “Total Atomic Charges”. In G03 and G09, atomic charges are labeled “Mulliken Atomic Charges”. Therefore find and change this label for the latter. PLEASE NOTE that Molekel will look for the title “Total Atomic Charges” so if your calculation was a geometry optimization then you have to find the set of charges that correspond to the last step of it. Look for the last string and change that one; you may also change them all with the right edition option in your editor, Molekel will use the last one since that should be the one corresponding to the optimized structure.
I’ll post something else when I find/remember it. Thanks for reading!