Life is Worth Living

Install Gromacs-2016.3 and Plumed-2.3.3

Monte Carlo molecular dynamics is…
I want to install plumed plugin of grmoacs to perform MCMD by gromacs.

Preparation

First of all, download Plumed-2.3.3 and Gromacs-2016.3. Plumed-2.3.3 has already provided offical patch of Gromacs-2016.3.

Decompress Plumed and Gromacs

1
2
tar -xvf gromacs-2016.3.tar.gz
tar -xvf plumed-2.3.3.tgz

Install Gromacs-Plumed

Install Plumed

1
2
3
4
./configure --prefix=/opt/plumed # install in prefix directory
make -j 4
make doc # this is optional and requires proper doxygen version installed
sudo make install

Patch Gromacs

PLUMED can be incorporated into gromacs using the standard patching procedure. Patching must be done in the gromacs root directory before the cmake command is invoked.

Patch with PLUMED using:

1
2
cd gromacs-2016.4
plumed patch -p
  1. amber14 4) gromacs-5.0.7 7) namd-2.8
  1. gromacs-2016.3 5) gromacs-5.1.4 8) namd-2.9
  2. gromacs-4.5.7 6) lammps-6Apr13 9) qespresso-5.0.2

Choose 2) gromacs-2016.3.

Install Gromacs

1
2
3
4
5
6
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2016.3
make
make check
sudo make install

Source GMXRC

1
source /opt/gromacs-2016.3/bin/GMXRC

Now, we can use gromacs with plumed patch.
http://plumed.github.io/doc-master/user-doc/html/trieste-4.html

0%