Category: biomedical theory

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Peptide Springiness By Terahertz Spectroscopy – An Upcoming Cover For Angewandte Chemie (And A POV-Ray File For Generating Springs)

image_m_anie201603825-toc-0001-m

From: onlinelibrary.wiley.com/doi/10.1002/anie.201603825/full

Image caption: An approach combining terahertz spectroscopy, X-ray diffraction, and solid-state density functional theory was utilized to accurately measure the elasticities of poly-l-proline helices by probing their spring-like vibrational motions. In their communication (DOI: 10.1002/anie.201602268), T. M. Korter and co-workers reveal that poly-l-proline is less rigid than commonly expected, and that the all-cis and all-trans helical forms exhibit significantly different Young's moduli.

Article: onlinelibrary.wiley.com/doi/10.1002/anie.201602268/abstract

Abstract: The rigidity of poly-l-proline is an important contributor to the stability of many protein secondary structures, where it has been shown to strongly influence bulk flexibility. The experimental Young's moduli of two known poly-l-proline helical forms, right-handed all-cis (Form-I) and left-handed all-trans (Form-II), were determined in the crystalline state by using an approach that combines terahertz time-domain spectroscopy, X-ray diffraction, and solid-state density functional theory. Contrary to expectations, the helices were found to be considerably less rigid than many other natural and synthetic polymers, as well as differing greatly from each other, with Young's moduli of 4.9 and 9.6 GPa for Forms I and II, respectively.

With thanks to Prof. Timothy Korter and Dr. Michael Ruggiero for letting me flex some rendering chops (and extra to Tim for knowing what he wanted to see early on).

The cover (well, a cover – they cram quite a bit of artwork into their journal nowadays) for this month's Angewandte Chemie highlights the correspondence between mechanical spring motion and the excitation of small alpha-helices by terahertz spectroscopy (a spectroscopic method capable of exciting small molecules at a low-enough frequency to excite the large-amplitude motions of, here, short peptides).

I was given a momentary pause on the way to coffee this morning listening to Chick Corea's Trilogy album when one of several of Brian Blade's solos reminded me of what Art Taylor said of being a great drummer. "Know the songs." There's a similarity between drum solos and science graphics – you can either do whatever-the-hell you want as long as it looks/sounds great, or you can take the effort to make both reference strongly back to the theme. Hearing the melody in a drum solo and extracting the key points of an article from just one image are not at all dissimilar. In both cases, you get reinforcement (to either direction) from the ones paying the most attention.

With that digression aside – you may have asked yourself, "Just how did he manage those smooth, reflective, luscious springs in POV-Ray" My suspicion was that someone must have rendered a spring in POV-Ray in the last decade and provided the .pov file in some directory somewhere online. That search eventually produced fruit in the form of a wonderful set of tutorials by Friedrich A. Lohmueller. The good news was that his file provided all the obvious basics – take a rendered sphere and make it walk a spiraling path along an axis, leaving images of itself all the way down until N number of coils were generated. The texture, lighting, color scheme, etc., were all secondary. That said, his .pov file references back into a few files for colors(.inc), finish(.ini), and textures(.inc) that made the .pov a little less portable if you didn't have a proper POV-Ray installed (and, being on a Mac, I'm still using MEGAPov until a miracle occurs and a new version of POV-Ray is released). These color/texture calls are just as easily embedded into the .pov file itself to make life easier. The result is the .pov file below, containing a reformed version of his original spring .pov file, some different labeling to point out where changes can occur, the call of colors by rgb, and blocked out [finish] sections so you can change the look of the spring to taste.

Download spring_somewhereville_dot_com.pov

// created by Friedrich A. Lohmueller, 2003 / 2010 / Jan-2011
// modified by Damian G. Allis, somewhereville.com, Mar-2016

// #include "textures.inc"

global_settings
	{
	assumed_gamma 1.0
	}

camera
	{
	angle 25                              //   smaller = closer
        location  < 0.0, 1.0, -5.0 >          //   -5.0 = distance to spring
        right x * image_width / image_height  //   want it larger --> go less neg.
        look_at < 0.0, 1.0, 0.0 >             //   want is smaller --> go more neg.
	}

light_source
	{
	< 1500, 2500, -2500 >
	color rgb < 1.0, 1.0, 1.0 >
	}

background 
	{
    color rgb < 1.0, 1.0, 1.0 >
	}

//
// begin the math to make the spring by spiraling a single sphere
//

#declare ampli = 0.50 ;                     // stretches and compresses the spring
#declare min_length = 0.80 ;
#declare mid_length = ampli + min_length ;
#declare time_test = 0.25 ;                 //0.25/0.75 shows max/min extention

#declare sprnglngth = mid_length + ampli * sin((clock + time_test) * 2 * pi) ;

#declare spiral =

union
	{
 	#local n_per_rev = 300 ;                   // spheres per spring revolution
 	#local n_of_rev = 4.00 ;                   // total coil count for the spring
 	#local h_per_ref = sprnglngth / n_of_rev ; // rise per revolution
 	#local nr = 0 ;                            // start loop
 	#while (nr < n_per_rev * n_of_rev)         // loop the spring sphere until...
    sphere
		{
    	< 0, -0.4, 0 > , 0.05                    // 0.05 adjusts the sphere diameter
    	translate< 0.25, -nr * h_per_ref / n_per_rev, 0.0 >
        rotate< 0, nr * 360 / n_per_rev, 0 >
		texture
			{
			pigment 
				{
				rgb < 0.658824, 0.658824, 0.658824 >
				}
            finish                               // adjust below to taste
        		{
            	ambient 0.050 
            	diffuse 0.500 
            	phong 0.1 
            	phong_size 2.500 
            	specular 0.500
		        reflection 0.15
		        brilliance 8
		        roughness 0.1
				}
			}
		}
	#local nr = nr + 1 ;
	#end
	} 

//
// end the math to make the spring by spiraling a single sphere
//

object
	{
	spiral translate< 0.0, 2.3, 0.0>       // translates "spiral" on the screen
	}

If you download the .pov file and run it, you should produce the spring image below – the fun is yours to make modifications to the file and see what those modifications do.

2016may13_spring

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GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox

Summarized below are the catches and fixes from a recent effort to build GROMACS 5.0.1 with FFTW3 (single- and double-precision) and GPU support (so, single-precision). Also, a trick I've been doing with great success lately, using a virtual machine to keep my real machine as clean as possible.

0. The Virtues Of VirtualBox

Open source means never having to say you're sorry.

I've made the above proclamation to anyone who'd listen lately who has any interest in using Linux software (because, regardless of what anyone says on the matter, it ain't there yet as an operating system for general scientific users with general computing know-how). You will very likely find yourself stuck at a configure or make step in one or more prerequisite codes to some final build you're trying to do, leaving yourself to google error messages to try to come up with some kind of solution. Invariably, you'll try something that seems to work, only to find it doesn't, potentially leaving a trail of orphaned files, version-breaking changes, and random downgrading only to find something else stupid (or not) fixed your build problems.

I've an install I'm quite happy with that has all of the working code I want on it working – and I've no interest in having to perform re-installs to get back to a working state again.

My solution, which I've used to great success with GAMESS-US, GROMACS, NWChem, and Amber (so far), is to break a virtual instance in VirtualBox first. For those who don't know (and briefly), VirtualBox lets you install a fully-working OS inside of your own OS that simply sits as a file in a Virtual VM folder in your user directory. My procedure has been to install a 60 GB VirtualBox instance of (currently) Ubuntu 14.04 (which I will refer to here as PROTOTYPE), fully update it to the current state of my RealBox (updates, upgrades, program installs, etc.), then copy PROTOTYPE somewhere else on the machine. The only limitation of this approach is that VirtualBox doesn't give you access to the GPU if you're testing CUDA-specific calculations. That said, it does let you install the CUDA Development Toolkit and compile code just fine, so you can at least work your way through a full build to make sure you don't run into problems.

When you're done trashing your VirtualBox after a particularly heinous build, just delete PROTOTYPE from Virtual VM and re-copy your copy back into Virtual VM – voila! You're ready for another build operation (or to make sure your "final" build actually works flawlessly before committing the build to your RealBox.

That's all I have to say on the matter. Consider it as your default procedure (at this point, I won't touch my RealBox with new installs until I know it's safe in VirtualBox).

1. The State Of My Machine Pre-GROMACS And All Other apt-get's Used Below

What follows below is pretty straightforward. Errors you might get that don't appear below might be related to the lack of certain installs on your machine that I installed on VirtualBox. That is, my standard PROTOTYPE comes standard with Intel's Fortran and C Compilers (for code optimization). Those installs required a few installs above the base Ubuntu install. These are (and are pretty standard anyway, so I say install them anyway): 

sudo apt-get install build-essential gcc-multilib rpm openjdk-7-jre-headless

I could have just installed a fresh version of 14.04 onto a machine to try this myself, but I'm not that motivated. Also, note this list does not include the all-important cmake. We'll get to that.

And for the rest of GROMACS (at least for older versions), there were lots of mesa/gnuplot/motif-specific dependencies in older versions of GROMACS to build all of the files included in the GROMACS package. Regardless of GPU builds or not, I tend to default to install all the packages below just to have them (which all, for 14.04, currently apt-get properly).

sudo apt-get install openmpi-bin openmpi-common gfortran csh grace menu x11proto-print-dev motif-clients freeglut3-dev libx11-dev libxmu-dev libxi-dev libgl1-mesa-glx libglu1-mesa libglu1-mesa-dev libgl1-mesa-dri libcurl-ocaml-dev libcurl4-gnutls-dev gnuplot

If you don't install the libblas3gf libblas-doc libblas-dev liblapack3gf liblapack-doc liblapack-dev series, you'll see the following note from your cmake steps in GROMACS.

— A library with BLAS API not found. Please specify library location.
— Using GROMACS built-in BLAS.
— LAPACK requires BLAS
— A library with LAPACK API not found. Please specify library location.
— Using GROMACS built-in LAPACK.

My own preference is to use the (assumedly newer) Ubuntu-specific libraries from apt-get.

sudo apt-get install libblas3gf libblas-doc libblas-dev liblapack3gf liblapack-doc liblapack-dev

GPU-Specific? One More apt-get

My first passes at proper GPU compilation involved several steps for the nVidia Developer Toolkit install. That's now taken care of with apt-get, so perform the final apt-get to complete the component/dependency installations.

sudo apt-get install nvidia-cuda-dev nvidia-cuda-toolkit

With luck, your first attempt at a GPU-based installation will look like the following:

[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
…
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable https://www.somewhereville.com/bin/gmx
[100%] Built target gmx

2. Nothing Happens Without cmake

Install cmake! Reproducing the output below to make sure you're using the same versions for everything (in the event something breaks in the future).

sudo apt-get install cmake

Reading package lists… Done
Building dependency tree
Reading state information… Done
The following packages were automatically installed and are no longer required:
linux-headers-3.13.0-32 linux-headers-3.13.0-32-generic
linux-image-3.13.0-32-generic linux-image-extra-3.13.0-32-generic
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
cmake-data
Suggested packages:
codeblocks eclipse
The following NEW packages will be installed:
cmake cmake-data
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 3,294 kB of archives.
After this operation, 16.6 MB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/main cmake-data all 2.8.12.2-0ubuntu3 [676 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/main cmake amd64 2.8.12.2-0ubuntu3 [2,618 kB]
Fetched 3,294 kB in 30s (106 kB/s)
Selecting previously unselected package cmake-data.
(Reading database … 258157 files and directories currently installed.)
Preparing to unpack …/cmake-data_2.8.12.2-0ubuntu3_all.deb …
Unpacking cmake-data (2.8.12.2-0ubuntu3) …
Selecting previously unselected package cmake.
Preparing to unpack …/cmake_2.8.12.2-0ubuntu3_amd64.deb …
Unpacking cmake (2.8.12.2-0ubuntu3) …
Processing triggers for man-db (2.6.7.1-1) …
Setting up cmake-data (2.8.12.2-0ubuntu3) …
Setting up cmake (2.8.12.2-0ubuntu3) …

3. First Pass At GROMACS

The make install step will place GROMACS where you want it on your machine, so you're just as good building in $HOME/Downloads as you are anywhere else. I will be performing all operations from $HOME/Downloads unless otherwise stated.

According to the GROMACS Installation Manual, your quick-and-dirty install need only involve the following:

$ tar xvfz gromacs-src.tar.gz
$ ls
gromacs-src
$ mkdir build
$ cd build
$ cmake ../gromacs-src
$ make

This allows you build "out-of-source" as they put it. Frankly, I just dive right into the GROMACS folder and have at it.

CMake Error: The source directory "/home/user/Downloads/gromacs-5.0.1/build" does not appear to contain CMakeLists.txt.
Specify –help for usage, or press the help button on the CMake GUI.

And did you see the above error? If so, you read the GROMACS quick-and-dirty procedure backwards. I'm not running it this way, so doesn't matter to what follows.

My first attempt at building GROMACS produced the following output from PROTOTYPE (reproducing all the text below).

user@PROTOTYPE:~$ cd Downloads/
user@PROTOTYPE:~/Downloads$ gunzip gromacs-5.0.1.tar.gz 
user@PROTOTYPE:~/Downloads$ tar xvf gromacs-5.0.1.tar

gromacs-5.0.1/README
gromacs-5.0.1/INSTALL
…
gromacs-5.0.1/tests/CppCheck.cmake
gromacs-5.0.1/tests/CMakeLists.txt 

user@PROTOTYPE:~/Downloads$ cd gromacs-5.0.1/
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF

NOTE: If you just run cmake, you'll get the following…

cmake version 2.8.12.2
Usage

cmake [options] cmake [options] …

… which is to say, cmake requires at least one option be specified. Above, I'm just using -DGMX_GPU=OFF to start the process.

The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc
— Check for working C compiler: /usr/bin/cc — works
— Detecting C compiler ABI info
— Detecting C compiler ABI info – done
— Check for working CXX compiler: /usr/bin/c++
— Check for working CXX compiler: /usr/bin/c++ — works
— Detecting CXX compiler ABI info
— Detecting CXX compiler ABI info – done
— Checking for GCC x86 inline asm
— Checking for GCC x86 inline asm – supported
— Detecting best SIMD instructions for this CPU
— Detected best SIMD instructions for this CPU – SSE2
— Try OpenMP C flag = [-fopenmp]
— Performing Test OpenMP_FLAG_DETECTED
— Performing Test OpenMP_FLAG_DETECTED – Success
— Try OpenMP CXX flag = [-fopenmp]
— Performing Test OpenMP_FLAG_DETECTED
— Performing Test OpenMP_FLAG_DETECTED – Success
— Found OpenMP: -fopenmp
— Performing Test CFLAGS_WARN
— Performing Test CFLAGS_WARN – Success
— Performing Test CFLAGS_WARN_EXTRA
— Performing Test CFLAGS_WARN_EXTRA – Success
— Performing Test CFLAGS_WARN_REL
— Performing Test CFLAGS_WARN_REL – Success
— Performing Test CFLAGS_WARN_UNINIT
— Performing Test CFLAGS_WARN_UNINIT – Success
— Performing Test CFLAGS_EXCESS_PREC
— Performing Test CFLAGS_EXCESS_PREC – Success
— Performing Test CFLAGS_COPT
— Performing Test CFLAGS_COPT – Success
— Performing Test CFLAGS_NOINLINE
— Performing Test CFLAGS_NOINLINE – Success
— Performing Test CXXFLAGS_WARN
— Performing Test CXXFLAGS_WARN – Success
— Performing Test CXXFLAGS_WARN_EXTRA
— Performing Test CXXFLAGS_WARN_EXTRA – Success
— Performing Test CXXFLAGS_WARN_REL
— Performing Test CXXFLAGS_WARN_REL – Success
— Performing Test CXXFLAGS_EXCESS_PREC
— Performing Test CXXFLAGS_EXCESS_PREC – Success
— Performing Test CXXFLAGS_COPT
— Performing Test CXXFLAGS_COPT – Success
— Performing Test CXXFLAGS_NOINLINE
— Performing Test CXXFLAGS_NOINLINE – Success
— Looking for include file unistd.h
— Looking for include file unistd.h – found
— Looking for include file pwd.h
— Looking for include file pwd.h – found
— Looking for include file dirent.h
— Looking for include file dirent.h – found
— Looking for include file time.h
— Looking for include file time.h – found
— Looking for include file sys/time.h
— Looking for include file sys/time.h – found
— Looking for include file io.h
— Looking for include file io.h – not found
— Looking for include file sched.h
— Looking for include file sched.h – found
— Looking for include file regex.h
— Looking for include file regex.h – found
— Looking for C++ include regex
— Looking for C++ include regex – not found
— Looking for posix_memalign
— Looking for posix_memalign – found
— Looking for memalign
— Looking for memalign – found
— Looking for _aligned_malloc
— Looking for _aligned_malloc – not found
— Looking for gettimeofday
— Looking for gettimeofday – found
— Looking for fsync
— Looking for fsync – found
— Looking for _fileno
— Looking for _fileno – not found
— Looking for fileno
— Looking for fileno – found
— Looking for _commit
— Looking for _commit – not found
— Looking for sigaction
— Looking for sigaction – found
— Looking for sysconf
— Looking for sysconf – found
— Looking for rsqrt
— Looking for rsqrt – not found
— Looking for rsqrtf
— Looking for rsqrtf – not found
— Looking for sqrtf
— Looking for sqrtf – not found
— Looking for sqrt in m
— Looking for sqrt in m – found
— Looking for clock_gettime in rt
— Looking for clock_gettime in rt – found
— Checking for sched.h GNU affinity API
— Performing Test sched_affinity_compile
— Performing Test sched_affinity_compile – Success
— Check if the system is big endian
— Searching 16 bit integer
— Looking for sys/types.h
— Looking for sys/types.h – found
— Looking for stdint.h
— Looking for stdint.h – found
— Looking for stddef.h
— Looking for stddef.h – found
— Check size of unsigned short
— Check size of unsigned short – done
— Using unsigned short
— Check if the system is big endian – little endian
— Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.1")
— Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so
— Looking for xmlTextWriterEndAttribute in /usr/lib/x86_64-linux-gnu/libxml2.so – found
— Looking for include file libxml/parser.h
— Looking for include file libxml/parser.h – found
— Looking for include file pthread.h
— Looking for include file pthread.h – found
— Looking for pthread_create
— Looking for pthread_create – not found
— Looking for pthread_create in pthreads
— Looking for pthread_create in pthreads – not found
— Looking for pthread_create in pthread
— Looking for pthread_create in pthread – found
— Found Threads: TRUE
— Looking for include file pthread.h
— Looking for include file pthread.h – found
— Atomic operations found
— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found
— Setting build user/date/host/cpu information
— Setting build user & time – OK
— Checking floating point format
— Checking floating point format – IEEE754 (LE byte, LE word)
— Checking for 64-bit off_t
— Checking for 64-bit off_t – present
— Checking for fseeko/ftello
— Checking for fseeko/ftello – present
— Checking for SIGUSR1
— Checking for SIGUSR1 – found
— Checking for pipe support
— Checking for isfinite
— Performing Test isfinite_compile_ok
— Performing Test isfinite_compile_ok – Success
— Checking for isfinite – yes
— Checking for _isfinite
— Performing Test _isfinite_compile_ok
— Performing Test _isfinite_compile_ok – Failed
— Checking for _isfinite – no
— Checking for _finite
— Performing Test _finite_compile_ok
— Performing Test _finite_compile_ok – Failed
— Checking for _finite – no
— Performing Test CXXFLAG_STD_CXX0X
— Performing Test CXXFLAG_STD_CXX0X – Success
— Performing Test GMX_CXX11_SUPPORTED
— Performing Test GMX_CXX11_SUPPORTED – Success
— Checking for system XDR support
— Checking for system XDR support – present
— Try C compiler SSE2 flag = [-msse2]
— Performing Test C_FLAG_msse2
— Performing Test C_FLAG_msse2 – Success
— Performing Test C_SIMD_COMPILES_FLAG_msse2
— Performing Test C_SIMD_COMPILES_FLAG_msse2 – Success
— Try C++ compiler SSE2 flag = [-msse2]
— Performing Test CXX_FLAG_msse2
— Performing Test CXX_FLAG_msse2 – Success
— Performing Test CXX_SIMD_COMPILES_FLAG_msse2
— Performing Test CXX_SIMD_COMPILES_FLAG_msse2 – Success
— Enabling SSE2 SIMD instructions
— Performing Test _callconv___vectorcall
— Performing Test _callconv___vectorcall – Failed
— Performing Test _callconv___regcall
— Performing Test _callconv___regcall – Failed
— Performing Test _callconv_
— Performing Test _callconv_ – Success
— checking for module 'fftw3f'
— package 'fftw3f' not found
— pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
CMake Error at cmake/gmxManageFFTLibraries.cmake:76 (MESSAGE):
Cannot find FFTW 3 (with correct precision – libfftw3f for mixed-precision
GROMACS or libfftw3 for double-precision GROMACS). Either choose the right
precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
advanced option to let GROMACS build FFTW 3 for you
(-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack
library (-DGMX_FFT_LIBRARY=fftpack).
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Configuring incomplete, errors occurred!
See also "/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeOutput.log".
See also "/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeError.log".

Lots of little things to address here. We'll get to the Boost problem later. Meantime, you can see the critical error is in (1) the lack of FFTW3 and (2) the lack of my specifically asking for -DGMX_BUILD_OWN_FFTW=ON in the cmake process.

NOTE: If you try to fix the FFTW3 problem as described above, you'll get the following error:

-GMX_BUILD_OWN_FFTW=ON

CMake Error: Could not create named generator MX_BUILD_OWN_FFTW=ON

Make sure to put the "D" in:

-DGMX_BUILD_OWN_FFTW=ON

4. If You Don't Use DGMX_BUILD_OWN_FFTW=ON To Build FFTW3…

This is a skip-able section if you're letting cmake do the dirty work (and letting cmake do it is preferred, at least for getting GROMACS built). In trying sudo apt-get install fftw*, you see (currently) the following: fftw2 fftw-dev fftw-docs

No good. So, the procedure is to build FFTW3 from source (which is just as easy as installing from .deb or .rpm files if you installed everything I mentioned above). That said, your attempts to build FFTW3 and build GROMACS may have run into several errors because of how you built FFTW3. Beginning with your extracting and prep for make:

user@PROTOTYPE:~/Downloads$ tar xvf fftw-3.3.4.tar 
user@PROTOTYPE:~/Downloads$ cd fftw-3.3.4/

Any of the combinations below produce the same error:

user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure 
user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure -enable-shared=yes
user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure --enable-threads --enable-float

checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes
…
config.status: executing depfiles commands
config.status: executing libtool commands 

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF -DFFTWF_LIBRARY='/usr/local/lib/libfftw3.a'

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc
…
— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found
…
— checking for module 'fftw3f'
— package 'fftw3f' not found
— pkg-config could not detect fftw3f, trying generic detection
Could not find fftw3f library named libfftw3f, please specify its location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g. -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
CMake Error at cmake/gmxManageFFTLibraries.cmake:76 (MESSAGE):
Cannot find FFTW 3 (with correct precision – libfftw3f for mixed-precision
GROMACS or libfftw3 for double-precision GROMACS). Either choose the right
precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the
advanced option to let GROMACS build FFTW 3 for you
(-GMX_BUILD_OWN_FFTW=ON), or use the really slow GROMACS built-in fftpack
library (-DGMX_FFT_LIBRARY=fftpack).
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Configuring incomplete, errors occurred!
See also "/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeOutput.log".
See also "/home/user/Downloads/gromacs-5.0.1/CMakeFiles/CMakeError.log".

Including –enable-shared takes care of this error and gets you to a successful GROMACS build.

user@PROTOTYPE:~/Downloads/fftw-3.3.4$ ./configure --enable-threads --enable-float --enable-shared

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
— Check for working C compiler: /usr/bin/cc
…
— Performing Test PTHREAD_SETAFFINITY
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so – found
…
— checking for module 'fftw3f'
— found fftw3f, version 3.3.4
— Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so
— Looking for fftwf_plan_r2r_1d in /usr/local/lib/libfftw3f.so – found
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_sse2 in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_avx in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_altivec in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_simd_neon in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_sse2 in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_sse in /usr/local/lib/libfftw3f.so – not found
— Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so
— Looking for fftwf_have_altivec in /usr/local/lib/libfftw3f.so – not found
CMake Warning at cmake/gmxManageFFTLibraries.cmake:89 (message):
The fftw library found is compiled without SIMD support, which makes it
slow. Consider recompiling it or contact your admin
Call Stack (most recent call first):
CMakeLists.txt:733 (include)

— Using external FFT library – FFTW3
— Looking for sgemm_
…
— Configuring done
— Generating done
— Build files have been written to: /home/user/Downloads/gromacs-5.0.1

And out of a first-pass GROMACS build…

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=OFF

Scanning dependencies of target libgromacs
[0%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwlzh.c.o
[0%] Building C object src/gromacs/CMakeFiles/libgromacs.dir/__/external/tng_io/src/compression/bwt.c.o
…
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable https://www.somewhereville.com/bin/gmx
[100%] Built target gmx

5. But You Let cmake Build FFTW3. So, Continuing The Build Process

With all of the dependencies above installed, the one note I wanted to address was that for Boost:

…
— Performing Test PTHREAD_SETAFFINITY – Success
— Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against Gromacs.
— Looking for zlibVersion in /usr/lib/x86_64-linux-gnu/libz.so
…

It certainly isn't a major issue, but I wanted to try to get an warning-free build. Installing Boost 1.56 produced the following negative result:

user@PROTOTYPE:~/Downloads/boost_1_56_0$ ./bootstrap.sh

Building Boost.Build engine with toolset gcc… tools/build/src/engine/bin.linuxx86_64/b2
Detecting Python version… 2.7
Detecting Python root… /usr
Unicode/ICU support for Boost.Regex?… not found.
Generating Boost.Build configuration in project-config.jam…

Bootstrapping is done. To build, run:

./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

– Command line help:
./b2 –help

– Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html

– Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html 

user@PROTOTYPE:~/Downloads/boost_1_56_0$ sudo ./b2 install

Performing configuration checks

– 32-bit : no (cached)
– 64-bit : yes (cached)
– arm : no (cached)
…
…failed updating 58 targets…
…skipped 12 targets…
…updated 11322 targets… 

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DGMX_DOUBLE=OFF
user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ make

[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_copyrite_gpu.cu.o
[0%] Building NVCC (Device) object src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
…
[7%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o
In file included from /home/user/Downloads/gromacs-5.0.1/src/gromacs/options/basicoptions.h:52:0,
from /home/user/Downloads/gromacs-5.0.1/src/gromacs/commandline/cmdlinehelpwriter.cpp:55:
/home/user/Downloads/gromacs-5.0.1/src/gromacs/options/../utility/gmxassert.h:47:57: fatal error: boost/exception/detail/attribute_noreturn.hpp: No such file or directory
#include
^
compilation terminated.
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o] Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Sadly, the solution is to then include -DGMX_EXTERNAL_BOOST=off and stick with the internal boost, which then "makes" just fine. One page references the use of -DGMX_INTERNAL_BOOST=on, but that produced the following:

CMake Warning:
Manually-specified variables were not used by the project:

GMX_INTERNAL_BOOST

— Build files have been written to: /home/user/Downloads/gromacs-5.0.1

There's more on this issue at: gerrit.gromacs.org/#/c/1232/ and t24960.science-biology-gromacs-development.biotalk.us/compiling-boost-problem-and-error-with-icc-t24960.html, but I've opted not to worry about it.

So, with Boost installed, I simply ignore it (and have not installed Boost on my RealBox).

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DGMX_EXTERNAL_BOOST=off

6. Finishing Step If All Above Goes Well: CUDA-Based GROMACS Build

If everything else above has gone smoothly (and if you ignored the Boost install. If you didn't, remember to add -DGMX_EXTERNAL_BOOST=off to the cmake below), you should be able to cleanly run a cmake for a GPU version of GROMACS (below, with the final result to be placed into /opt/gromacs_gpu. You then specify the $PATH after and run with it).

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ cmake -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs_gpu -DGMX_BUILD_OWN_FFTW=ON

— The C compiler identification is GNU 4.8.2
— The CXX compiler identification is GNU 4.8.2
…
— Generating done
— Build files have been written to: /home/damianallis/Downloads/gromacs-5.0.1 

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ make

The make starts with the FFTW3 download and build…

Scanning dependencies of target fftwBuild
[ 0%] Performing pre-download step for 'fftwBuild'
— downloading…
src='http://www.fftw.org/fftw-3.3.3.tar.gz'
dest='/home/damianallis/Downloads/gromacs-5.0.1/src/contrib/fftw/fftw.tar.gz'
— [download 0% complete]
…
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable https://www.somewhereville.com/bin/gmx
[100%] Built target gmx

Finally, your (sudo) make install places everything into /opt/gromacs_gpu.

user@PROTOTYPE:~/Downloads/gromacs-5.0.1$ sudo make install

— The GROMACS-managed build of FFTW 3 will configure with the following optimizations: –enable-sse2
— Configuring done
— Generating done
— Build files have been written to: /home/damianallis/Downloads/gromacs-5.0.1
[1%] Built target fftwBuild
…
[100%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o
Linking CXX executable https://www.somewhereville.com/bin/gmx
[100%] Built target gmx