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Hi there, welcome to my page!
This is not a very flashy homepage, and you shouldn't expect to find flying things, sound, or nice colors. I will use this space to put stuff that may be useful for me and others, primarily materials for my different courses here at USP. If you want to get to the materials for the courses, follow the links below. Other links are further down. Except for the course materials, which I'll try to keep up to date and current, the other stuff is always under construction...
Guillermo
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Courses - Research - NMR Links - Modeling Links - Linux Links - Beowulf Links
Materials for courses I teach here at USP
The following links go to the subdirectories of courses I teach or taught. Here you will find all the information relevant to these courses. For many of the materials posted in these pages you will need a copy of Adobe Acrobat reader installed in your computer. Sorry, no solutions to current homework problems...
- Current Courses
Organic Chemistry (211/212)- Old Courses
Modern NMR (CH455) - Applied Spectroscopy (CH767)
Biochemistry (CH341)
Principles Lab (CH113)
Principles lab (CH114)
Research occupies a considerable portion of my interests, and therefore I have a page exclusively dedicated to the research activities and projects of the Moyna Group. In it you will find descriptions of the different project, links to current publications and posters presented in different conferences, information on current members of the group, and information on how to become a member of the group.
Follow this link to go directly to the Moyna Group Research Page.
- Our NMR resources
In February of 2000 we had our old and beaten up Varian EM390 CW-NMR spectrometer upgraded to an Anasazi EFT-90 spectrometer. We now have full FT-capabilities, including a 1H-13C probe, multiple pulse programming, 2D, etc., etc. A picture of our upgraded NMR spectrometer can be found here.
The instrument is used by researchers to perform daily NMR analyses of synthetic organic samples, as well as by students in our regular courses. Some of the courses that employ the EFT-90 include Principles or Chemistry, Principles of Organic Chemistry, Chemical Characterization, Chemical Synthesis, and Applied Spectroscopy. If you are interested, you can visit the Moyna Group NMR Software Site, which has a collection of pulse programs, C++ code, and Perl scripts for use with the EFT-90.
We will also aqcuire a high-resolution 400 MHz NMR spectrometer in the year 2001. The funds for the purchase and installation of this top-notch research instrument were obtained through an NSF grant, and will be matched by USP. The instrument will be the flagship of the Undergraduate NMR Program at USP. Follow the link to learn more about it.
- General NMR links
www.nmr.de - A nice collection of general NMR resources. There are several NMR courses, including some problem sets (if your German is good...), and a nice MRI introduction.
A link to the NMR periodic table. This has magnetic properties of all NMR sensitive nuclei.
- NMR vendors
The big boys, Varian and Bruker, in the USA and in Germany.
Also in the NMR making business are JEOL (USA), Tecmag, MR Resources, and Anasazi Instruments. These last guys are REALLY cool...
Most of the projects in the Moyna Group and Zauhar Group involve heavy use of molecular modleing applications. To find out how we use these programs and what we use them for, go to our research pages. Here you will find links to general molecular modeling resources.
- General modeling links
If you want to get the basics of what molecular modeling can do, the Center for Molecular Modeling (CMM) at NIH has a very nice on-line course on molecular modeling basics.
The CMM also maintains a large collection of links to tutorials for different packages.
Finally, visit Information from the Net page, part ot the AMBER web-page at UCSF. This site has an extensive collection of links to molecular modelling related sites.
- Molecular modeling packages
One of the packages we use most of the time is Sybyl, a suite of molecular modeling tools which also include impresive visualization tools, etc., etc. You can see what Sybyl and other related programs do at the Tripos web-page.
Another large and very complete package is Insight II (and related packages), produced by Molecular Simulations, Inc. (MSI). Visit their web-page to check out the capabilities of the program suite.
If you are interested in tools for desktop computers, you may find HyperChem and related programs useful. HyperChem has tools for molecular mechanic, semi-empirical, and ab initiocalculations. Visit the HyperCube we-page to learn more about them.
Antoher vendor with both workstation and desktop molecular modeling programs is Wavefunction. They make the popular Spartan package, which is ported to Windows, MacOS, and UNIX systems. The program can do MM, MD, and QM calculations.
If you are not willing to spend a lot of money in a molecular mechanics package, why not getting one for free? The Tinker package, maintained by Jay Ponder at Washington University in Saint Loius, is a very nice molecular mechanics package for simulations with peptides that has many nice capabilities (MM, MD, etc.). The only caveat, no GUI...
No collection of links to molecular modeling packages would be complete without one to the AMBER web-page. AMBER, developed and maintained by the Kollman Group at UCSF, is the grandaddy of the molecular simulation packages for proteins and nucleic acids, and has implementations of the latests developments in the field. A must have if you are doing protein and DNA simulations. Except for xleap, there is no GUI for AMBER...
Linux, perhaps the best next thing after DOS 3.3 (remember that?), is now ported to several systems, including Pentium, Aplha, MIPS, and, yep, Macs (68K and PPC). These are some links to this great (and free!) OS.
- Linux Distributions
The RedHat site, which probably has the most popular distributions package. Although it is safer to buy the CD-ROM from them, you can install the whole package from the web WITHOUT having to deal with cumbersome ftp stuff. Here is a description of how to do this.
Follow this link for the Slackware site, which has another very popular distribution. Theirs has an AppleTalk server RPM, which is pretty good if you want to share Apple devices with your LINUX box.
Some other distributions are Debian, an Open Source site and has tons of software packages, as well as the Mandrake distribution combo.
- Linux software and sites
Due to the Open Source philosophy, there are zillions of sites with Linux stuff out there, way to many to be listed here. However, here are a few to start your surfing for Linux resources.
- Linux-ready systems
Also, you may be interested in checking vendors of 'LINUX-ready' systems.
TheLinuxStore.com has a very cheap entry system, the PIA, for 400 bucks. They also have larger systems, as well as parts for the do-it-yourselvers.
For larger, number crunching applications, Mycroway has a very nice systems, including Intel and Alpha based systems, pre-loaded with Linux as well as Windows-NT (ugh...).
In addition to these two, which are the ones I check regularly, www.linux.org has a huge list of vendors of Linux ready-systems.
If you want to build a supercomputer in your kitchen table while you warm up that leftover chilli with beans and those delicious 85-cent-a-bag hotdogs, this is the way to go. A beowulf is basically a 'pile-of-PCs' clustered together that work in parallel and perform, in some cases, better that comercial supercomputers in the US$ 100,000 to 1,000,000 range.
Here at USP we have built two Beowulf clusters. The first one, minigang, was a test system to study the feasibility of building a larger cluster. With literally no money, we were able to get the same computing punch than a Silicon Graphics O2 R10000 workstation for certain computational chemistry applications (GAMESS).
We have now completed our
second Beowulf cluster, minigang's big brother, chaingang.
Chaingang is a 16-node plus server cluster. You can read all about chaingang
on its own homepage.
Courses - Research - NMR Links - Modeling Links - Linux Links - Beowulf Links
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