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Example input for the Wales Group code
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# Getting started with GMIN, OPTIM and PATHSAMPLE These directories contain example input and output for the **GMIN**, **OPTIM** and **PATHSAMPLE** codes developed in the Wales Group at the University of Cambridge. ## Prerequisites In order to run through these examples, you will need to either use a build of the Wales Group VM (available for VirtualBox [here](http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova)), or have the following Ubuntu packages installed via `apt-get`: - to compile the code ``` sudo apt-get install build-essential gfortran cmake cmake-curses-gui csh bison flex libblas-dev liblapack-dev ``` - utility programs for visualisation etc ``` sudo apt-get install vim git subversion gnuplot-x11 gv ``` Acquiring the source code for **GMIN**, **OPTIM** and **PATHSAMPLE** and compiling the code using **cmake** is discussed in detail below. ## Example systems ### [LJ38](./LJ38) - a 38 atom Lennard-Jones cluster <img src="LJ38/lj38_gmin.png" width="50%", height="50%"> - Basin-hopping with **GMIN** - Calculating the mean first encounter time (MFET) - Connecting minima with a discrete path using **OPTIM** - Setting up a **PATHSAMPLE** database using an **OPTIM** *path.info* file - Expanding a **PATHSAMPLE** database in a targeted way ### [tetra-ALA](./tetra_ALA) - an alanine polypeptide (AMBER) <img src="tetra_ALA/tetra_ALA_igb2_gmin.png" width="50%", height="50%"> - Basin-hopping with **A12GMIN** - Investigating the effect of removing C-alpha chirality checks - Connecting minima with a discrete path using **A12OPTIM** - Setting up a **PATHSAMPLE** database using an **A12OPTIM** *path.info* file - Expanding a **PATHSAMPLE** database in a targeted way ### [SER-LYS](./SER_LYS) - a capped dipeptide (AMBER) <img src="SER_LYS/ser_lys_fe0.6_gmin.png" width="50%", height="50%"> - Basin-hopping with **GMIN** - Free energy basin-hopping using **A12GMIN** to investigate the effect of entropy ### [trypzip](./trypzip) - a 12 residue tryptophan zipper (AMBER) <img src="trypzip/trypzip_endpoints.png" width="50%", height="50%"> **CHALLENGE!** - Efficiently expand a **PATHSAMPLE** database for a provided initial folding path - Requires much trial and error! ## Compiling the Wales Group codes ### Obtaining the source code The source code can be obtained from the Wales group website [here](http://www-wales.ch.cam.ac.uk/svn.tar.bz2) or using `wget` like so: ``` wget http://www-wales.ch.cam.ac.uk/svn.tar.bz2 ``` **NOTE:** Due to licensing issues, we cannot distribute the **AMBER** or **CHARMM** interfaced versions of our source code. If you have a license for either, contact [David Wales](mailto:dw34@cam.ac.uk) and request access to the restricted code. Copy the tar file into a working directory and uncompress it as follows: ``` tar xvfj svn.tar.bz2 ``` Replace the file name as necessary should you have a version of the source containing the AMBER or CHARMM interface. Now, change directory until you see a set of folders including one for **GMIN**, one for **OPTIM** and one for **PATHSAMPLE**. ### Compiling GMIN All **cmake** builds are 'out of source' i.e. we build the binary in a directory that does not contain the source code. As a result, the first thing we need to do is create a build directory and move into it (note the nifty shortcut!): ``` mkdir -p GMIN/build/gfortran cd !$ ``` In this example, we are going to build vanilla **GMIN** using **gfortran**. First, we run **cmake** specifying the compiler using the `FC` environment variable and the source directory: ``` FC=gfortran cmake ../../source ``` You should see some output similar to the following: ``` energy@landscapes:~/workshop/code/GMIN/build/gfortran$ FC=gfortran cmake ../../source -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- 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 -- The Fortran compiler identification is GNU -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes FC_PROGNAME = gfortran Compiler switch = gfortran Setting initial values for compiler flags CMAKE_Fortran_COMPILER = /usr/bin/gfortran /home/energy/workshop/code/CMakeModules/FindMYBLAS.cmake: creating BLAS library. /home/energy/workshop/code/CMakeModules/FindMYLAPACK.cmake: creating LAPACK library. -- Configuring done -- Generating done -- Build files have been written to: /home/energy/workshop/code/GMIN/build/gfortran ``` To see additional options for the compilation (including enabling the interfaces to **AMBER** and **CHARMM**) you can run ``ccmake .`` in your build directory. If you make any changes here, make sure you 'configure' (`c`), 'exit' (`e`) and then 'generate' (`g`). You may need to do this twice for some builds. Pressing `q` will quit without making changes. Assuming you didn't see any errors - you're now ready to compile **GMIN** as follows, replacing `X` with the number of cores (found by typing `nproc`). If in doubt, use 1: ``` make -jX ``` This may take some time depending on how many cores you have available. When it's done, you should see a **GMIN** binary in the build directory: ``` ... Scanning dependencies of target GMIN [100%] Building Fortran object CMakeFiles/GMIN.dir/main.F.o Linking Fortran executable GMIN [100%] Built target GMIN energy@landscapes:~/workshop/code/GMIN/build/gfortran$ ls CMakeCache.txt cmake_install.cmake GMIN libgminlib.a libmbpol libmylapack.a modules CMakeFiles display_version.f90 libextralib.a liblibmbpol.a libmyblas.a Makefile porfuncs.f90 ``` Finally, move the binary into your `$PATH` so that you can run it anywhere by simply typing `GMIN`. If you have access to the **AMBER** or **CHARMM** interfaces source code or a different compiler, you may wish to build a different version of **GMIN**. A few examples for specific builds are provided here for reference, but this list is not comprehensive: - **A12GMIN** (GMIN with AMBER12) using the ifort compiler: ``` mkdir -p GMIN/builds/ifort_amber12 cd !$ FC=ifort cmake -DWITH_AMBER12=1 ../../source make -jX ``` - **C35GMIN** (GMIN with CHARMM 35) using the pgf90 compiler: ``` mkdir -p GMIN/builds/pgi_charmm35 cd !$ FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source make -jX ``` - **CUDAGMIN** (GMIN leveraging GPU minimisation via the AMBER 12 interface) using the ifort compiler: ``` mkdir -p GMIN/builds/ifort_cuda cd !$ FC=ifort cmake -DWITH_CUDA=1 ../../source make -jX ``` **NOTE:** requires the **CUDA** toolkit to be installed at version 5.5 or higher. ### Compiling OPTIM Like **GMIN** above, **OPTIM** is easily compiled with **cmake**. Skipping straight to the examples (replace `X` by the number of cores to use): - **OPTIM** with the gfortran compiler ``` mkdir -p GMIN/build/gfortran cd !$ FC=gfortran cmake ../../source make -jX ``` - **A12OPTIM** (OPTIM with AMBER12) using the ifort compiler: ``` mkdir -p OPTIM/builds/ifort_amber12 cd !$ FC=ifort cmake -DWITH_AMBER12=1 ../../source make -jX ``` - **C35OPTIM** (OPTIM with CHARMM 35) using the pgf90 compiler: ``` mkdir -p OPTIM/builds/pgi_charmm35 cd !$ FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source make -jX ``` - **CUDAOPTIM** (OPTIM leveraging GPU via the AMBER 12 interface) using the ifort compiler: ``` mkdir -p OPTIM/builds/ifort_cuda cd !$ FC=ifort cmake -DWITH_CUDA=1 ../../source make -jX ``` **NOTE:** requires the **CUDA** toolkit to be installed at version 5.5 or higher. ### Compiling PATHSAMPLE **PATHSAMPLE** has very limited build options as it does not interface with any specific potential. To ensure binary file formats are readable, you should be using the same compiler for both **OPTIM** and **PATHSAMAPLE**! Again replacing `X` with the number of cores in the examples below: - **PATHSAMPLE** using the gfortran compiler ``` mkdir -p PATHSAMPLE/builds/gfortran cd !$ FC=gfortran cmake ../../source make -jX ``` - **PATHSAMPLE** using the NAG compiler ``` mkdir -p PATHSAMPLE/builds/nagfor cd !$ FC=nagfor cmake ../../source make -jX ``` ### Compiling disconnectionDPS **disconnectionDPS** is used to createdisconnectivity graphs from **PATHSAMPLE** databases. It can be compiled in a single step from the source as follows: ``` cd DISCONNECT/source gfortran -o disconnectionDPS disconnectionDPS.f90 ``` ### Compiling utility programs There are a few utility programs that you might need to specific examples. The code and compilation instructions for these can be found [here](./utilities).
