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Installing Plumed

Plumed is an exiting “new” rare-event code that is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

However with the advent of PLUMED2 – v2.0.1 in late 2013, the code had major changes for the user interface. Over the next few posts I will provide Installations and basic user guides for the new version of Plumed.

1. Installing Libraries

Before you install Plumed you need to install BLAS and LAPAC libraries. You can download them together at – http://www.netlib.org/lapack/#_software. Download “lapack-3.5.0”. Put them in the relevant directory and unzip the folder.

Installing BLAS

Step 1 – cd /lapack-3.5.0/BLAS/SRC

Step 2 – Compile all of the .f files to produce .o files
g77 -c -O3 *.f

Step 3 – Combine the .o files into a library
ar rv libblas.a *.o

Step 4 – Switch to root and install
cp libblas.a /usr/local/lib

Installing LAPACK

Step 1 – cd /lapack-3.5.0/

Step 2 – You can either use pre-compiled installation. Copy the appropriate make.inc.XXX file from the INSTALL directory into make.inc in the main directory.
Example: cp INSTALL/make.inc.LINUX make.inc
OR
./Cmake

Step 3 – sudo make

Step 4 – sudo make install

2. Installing Plumed

Step 1 – Download Plumed from http://plumed.github.io/doc-v2.0/user-doc/html/_installation.html

Step 2 – cd /plumed-2.0.2

Step 3 – ./configure.sh -ldl -L/usr/local/lib/liblapack.a -llapack -D__PLUMED_HAS_LAPACK -L/usr/local/lib/libblas.a -lblas -D__PLUMED_HAS_BLAS SOEXT=dylib
Select – 3> mac.mpi.clang

Step 4 – Remove flag “-lmpi_cxx” from variable DYNAMIC_LIBS in Makefile.conf

Step 5 – source sourceme.sh

Step 6 – sudo make

Step 7 – sudo make install

To uninstall, remove the following files and directories:
/usr/local/lib/plumed/
/usr/local/include/plumed
/usr/local/bin/plumed
/usr/local/bin/plumed-mklib
/usr/local/bin/plumed-newcv
/usr/local/bin/plumed-patch
/usr/local/lib/libplumed.dylib
/usr/local/lib/libplumedKernel.dylib

3. Installing Gromacs

We are going to install a mpi version of double precision gromacs with plumed.
For more information on custom Gromacs installation – http://dqfnet.ufpe.br/groups/geekstuff/wiki/2ebb2/
Also Plumed has been tested with a few verions of Gromacs. Ofcourse you can try a different version but it is safest to use the one recommended.

Step 1 – Get gromacs-4.6.5. http://www.gromacs.org/Downloads

Step 2 – cp /patches/patch.sh .
-> 2) gromacs-4.6.5

Step 3 – Make a directory to compile Gromacs. Usually this is recommended as you can end up multiple version of Gromacs in the same machine.
mkdir build
cd build

Step 4 – Make a version of Gromacs with the correct ingredients. Like this is a double precision version with MPI.
CMAKE_PREFIX_PATH=/usr/local/include:/usr/local/lib:/opt/local/:/usr/local/bin cmake .. -DGMX_X11=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6.5_double/ -DGMX_DOUBLE=ON -DGMX_MPI=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DMX_GSL=ON -DMX_THREAD_MPI=ON -DGMX_CPU_ACCELERATION=SSE2 -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_OWN_FFTW=ON

Step 5 – sudo make

Step 6 – sudo make install

4. Installing Gromacs in Linux

Follow the same steps as above.

CMAKE_PREFIX_PATH=/usr/local/include:/usr/local/lib:/opt/local/:/usr/local/bin cmake .. -DGMX_X11=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6.5_double/ -DGMX_DOUBLE=ON -DGMX_MPI=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DMX_GSL=ON -DMX_THREAD_MPI=ON -DGMX_CPU_ACCELERATION=SSE2 -DREGRESSIONTEST_DOWNLOAD=ON

5. Citing PLUMED

You may wish to cite the following reference if you have utilized PLUMED in your work:
1. M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Parrinello.
2. PLUMED: a portable plugin for free-energy calculations with molecular dynamics, Comp. Phys. Comm. 2009 vol. 180 (10) pp. 1961-1972.