Computational Chemistry sandwich placement available

It is that time of year again when I can announce my group at AstraZeneca has a new position available. We are looking for a Sandwich Student to join us in September 2012. We successfully rebooted our sandwich student program last year. The ideal candidate will currently be in the second year of their chemistry or computer science degree. No experience is required, but a willingness to learn is crucial as you will learn about cheminformatics and computational chemistry.

Unfortunately, I personally will not be involved with this student, apart from the recruitment process for reasons which are subject to another blog post.

If you are interested find out more here: http://www.ideas.astrazeneca.com/sandwich-and-summer-placements/ and search for reference: TRES DS 12. Closing date for applications is 25th Jan 2012. Good luck!

Photo courtesy of http://www.flickr.com/photos/53921113@N02/5645102295/

Computational Chemistry sandwich placement available

I'm delighted to announce we have a 12 month placement available for a sandwich student. Typically the third year of a four year undergraduate degree. It has been a while since my department has had a placement student, but I firmly believe the experience is valuable for both the student and us. I did a placement during my undergraduate degree and thoroughly enjoyed it. Seemingly my employer agreed as they later sponsored my PhD.

The ideal candidate would be a chemist or computer scientist. The only skill you need to bring is a desire to learn. We don't expect you to know all about drug discovery or be an amazing programmer. During the placement you will have to the opportunity to pick up the skills required to make a meaningful contribution to our department.

If you are interested find out more here, http://www.ideas.astrazeneca.com/sandwich-and-summer-placements/ and search for reference: TRES DECS 11. Closing date for applications is 15th Feb 2011. Good luck!

Install CPMD

CPMD is massively parallel code. There is little point running it serially as it will literally take forever to do anything useful. I'm providing the instructions I used to compile the parallel version on our HPC facility, therefore they may need altering for your computer.

Some technical details:

• CPMD 3.13.1
• Intel compilers/MKL 10.1
• openSUSE 10.3, 64-bit

cd SOURCE
./mkconfig.sh IFORT-AMD64-MPI > Makefile

# In Makefile alter
FFLAGS = -pc64 -O2 -unroll
LFLAGS = -L/opt/intel/mkl/10.0.3.020/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
CC = mpicc -cc=icc
FC = mpif90 -fc=ifort -c
LD = mpif90 -fc-ifort -i-static

Run make, hopefully it will compile happily, copy cpmd.x to somewhere on your $PATH.

It would be wise to test your binary. First download cpmd-test.tar.gz from the contrib section of the downloads (tests are not included with the source). Run as mpisub 5x2 cpmd.x inp-1 or similiar depending on your setup. This command would use 5 dual processor computers.

Chemistry on the iPhone

The iPhone has had plenty of press since it's initial announcement. In my view, one of the best features is the App store. With some 15,000 applications currently available there is something for everyone - including Chemists! From straight reference to 3D visualisation with touch interface these applications demonstrate what scientists could do on a smartphone. This is by no means an extensive list, but some apps that have caught my eye:

• Molecules (iTunes link)
  
• iMoleBuilder (iTunes link)
  
• The Chemical Touch (iTunes link)
  
• miMol (iTunes link)
  
• Atom in a box (iTunes link)
  
• Solutions (iTunes link)
  
• Wikipanion (iTunes link) - Not specifically for Chemistry, but lots of chemical data is now available on Wikipedia.

The App Store categories is the obvious way to find these, specifically in Education, Reference or Utilities. However, Solutions falls under Health & Fitness!

Anyone can write an App for the iPhone (and iPod Touch) using the SDK. It is Objective-C, not something I'm familiar with so that goes on my to do list for post-thesis!

Other smartphones are also introducing SDK's as well, e.g. Android. The mobile platform is becoming an increasingly important development arena. It is good to see that Chemistry has a presence there too.

Academic software

Although there is lots of excellent open source software available for computational chemistry and cheminformatics one would be narrow minded if they ignored the large array of commercial software also available.

Unfortunately, in an academic setting the cost of this software is far beyond the limited budgets available. Most companies offer discounted prices for academia, which is great, but some have gone further. Namely, ChemAxon and OpenEye offer free academic licenses.

So if you're in academia and fancy getting your hands on commerical software I'd follow these links:

• ChemAxon
• OpenEye

GROMACS 4

GROMACS 4 was recently released. Installing using the Intel compilers and MKL for FFTW was the same as with 3.3.3.

See my previous post for full instruction. Please note the lines to change in configure are now 26595 and 26663.

Also note the test set hasn't been updated for version 4, so keep and eye out for that.

Compile GROMACS with Intel compilers

I recently installed GROMACS on our condor pool. Unsurprisingly code that runs so fast is very dependent on the numerical libraries used during compilation. I therefore chose to use Intel MKL and Intel compiler as they perform very well together. Unfortunately the configure file is not suitable for Intel 10.1 users. I am using GROMACS 3.3.3 (although I hear version 4 should be out imminently), on 32-bit openSUSE 10.3.

First edit your configure file, lines 25897 & 25965:

Alter
LIBS="-lmkl $LIBS"
to
LIBS="-lmkl_intel -lmkl_sequential -lmkl_core $LIBS"

Then run:
./configure CC="icc" CPPFLAGS="-I/opt/intel/mkl/10.0.3.020/include" LDFLAGS="-L/opt/intel/mkl/10.0.3.020/lib/32" --with-fft=mkl
make
make install

You may need to alter the version number or location of your MKL files. I recommend you also download the test set to confirm the compilation. I have 4 fails, but closer inspection revealed they were not show stoppers.