GROMACS 5.1.4 PLUMED 2.3.5 ¶

Installation Date: 14/06/2018
URL: http://www.gromacs.org/
- Installed on: Apolo II
License: GNU Lesser General Public License (LGPL), version 2.1.

Table of Contents

GROMACS 5.1.4 PLUMED 2.3.5

Dependencies ¶

GNU GCC >= 5.4.0
Mpich2 >= 3.2
Python >= 2.7.15 (Miniconda)
OpenBLAS >= 0.2.19
CUDA >= 9.0 (have to include SDK)
Plumed >= 2.3.5
Boost >= 1.67.0

Installation ¶

After resolving the aforementioned dependencies, you can proceed with the installation of GROMACS.

Download the latest version of GROMACS

$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.4.tar.gz
$ tar -zxvf gromacs-5.1.4.tar.gz

After unpacking GROMACS, we continue with the following configuration and compilation steps:

Note

You have to load all the apps in the dependencies, or add them to the PATH, we are assuming that all is done
```
$ cd gromacs-5.4.1
$ plumed patch -p --shared #select the fifth option
$ mkdir build
$ cd build
```

compile it

$ CC=mpicc CXX=mpicxx FC=mpif90 cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/share/apps/cuda/9.0
    -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs/5.1.4/gcc-5.4.0_plumed-2.3.5
    -DGMX_EXTERNAL_BLAS="/share/apps/openblas/0.2.19/gcc/5.4.0/lib/libopenblas.so"
    -DGMX_BUILD_OWN_FFTW=ON -DGMX_EXTERNAL_BOOST=ON
    -DBoost_INCLUDE_DIR="/share/apps/boost/1.67.0/gcc-5.4.0_mpich2-3.2/include"
    -DBoost_LIBRARY_DIRS="/share/apps/boost/1.67.0/gcc-5.4.0_mpich2-3.2/lib"
    -DBoost_DIR="/share/apps/boost/1.67.0/gcc-5.4.0_mpich2-3.2" -DNVML_INCLUDE_DIR=/share/apps/cuda/9.0/include
    -DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON  -DREGRESSIONTEST_DOWNLOAD=ON  2>&1 | tee gromacs-cmake.log
$ make 2>&1 | tee gromacs-make.log
$ make check 2>&1 | tee gromacs-check.log
$ make install 2>&1 | tee gromacs-make-install.log

Use mode ¶

To run Gromacs + Plumed it is necessary to have the following files: - plumed.dat - md_1B2S_AA27K.tpr

Definition of input files

# set up two variables for Phi and Psi dihedral angles
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
#
# Activate metadynamics in phi and psi
# depositing a Gaussian every 500 time steps,
# with height equal to 1.2 kJoule/mol,
# and width 0.35 rad for both CVs.
#
metad: METAD ARG=phi,psi PACE=500 HEIGHT=1.2 SIGMA=0.35,0.35 FILE=HILLS
# monitor the two variables and the metadynamics bias potential
PRINT STRIDE=10 ARG=phi,psi,metad.bias FILE=COLVAR

References ¶

Gromacs instructions. Retrieved July 10, 2019, from http://www.gromacs.org/Documentation/Installation_Instructions_5.0
Gromacs github. Retrieved July 10, 2019, from https://github.com/gromacs/gromacs/blob/master/cmake/FindNVML.cmake
Lindqvist. Retrieved July 10, 2019, from http://verahill.blogspot.com.co/2013/04/396-compiling-gromacs-46-with-openblas.html
Compiling GROMACS on Cluster. Retrieved July 10, 2019, from https://ringo.ams.stonybrook.edu/index.php/Compiling_GROMACS_on_Cluster
Lindqvist.Retrieved July 10, 2019, from http://verahill.blogspot.com/2012/03/building-gromacs-with-fftw3-and-openmpi.html
How to compile gromacs. Retrieved July 10, 2019, from https://mini.ourphysics.org/wiki/index.php/How_to_compile_Gromacs
Github issue. Retrieved July 10, 2019, from https://github.com/linux-sunxi/linux-sunxi/issues/62
Nvidia gromacs. Retrieved July 10, 2019, from https://ngc.nvidia.com/catalog/containers/hpc:gromacs
Running VASP on Nvidia GPUs. Retrieved July 10, 2019, from https://www.nsc.liu.se/~pla/
Gromacs (GPU). Retrieved July 10, 2019, from http://www.hpcadvisorycouncil.com/pdf/GROMACS_GPU.pdf

Authors ¶

Mateo Gómez Zuluaga

GROMACS 5.1.4 PLUMED 2.3.5¶

Dependencies¶

Installation¶

Use mode¶

References¶

Authors¶