GROMACS-LS 4.5.5 ¶

Table of Contents

GROMACS-LS 4.5.5

Basic information ¶

Official Website: https://www.mdstress.org/index.php/gromacs-ls/
License: GNU General Public License (GPL), version 2.
Installed on: Apolo II

Tested on (Requirements)¶

OS base: CentOS (x86_64) $\boldsymbol{\ge}$ 6.6 (Rocks 6.2)
Compiler: GCC 5.4.0
Math Library: FFTW 3.3.5
Others: LAPACK Version 3.5.0

Installation ¶

The following procedure presents the way to compile GROMACS-LS 4.5.5 for local stress calculations from molecular simulations. [1]

Note

For the building, the GCC compiler version 5.4.0 was used due to better compatibility with FFTW3 and LAPACK.

Load the necessary modules for the building.
```
$ module load cmake/3.7.1 \
              gcc/5.4.0 \
              fftw/3.3.5_gcc-5.4.0_openmpi-1.8.8-x86_64 \
              lapack/3.5.0_gcc-5.4.0
```
Note

LAPACK V3.5.0 is the recommended version of LAPACK from GROMACS-LS, you can see how to install it in our Scientific Libraries section or here LAPACK 3.5.0.

Download the latest version of GROMACS-LS

$ wget https://www.mdstress.org/files/4314/6351/1328/gromacs-4.5.5-ls-5.0.tar.gz
$ tar xfz gromacs-4.5.5-ls-5.0.tar.gz

Inside the folder, on the top create a build directory where the installation binaries will be generated by cmake.
```
$ cd gromacs-4.5.5-ls-5.0
$ mkdir build
$ cd build
```
Execute the following commands, those will export the environmental variables that GROMACS-LS needs for compilation.
```
$ export FFTW3_ROOT_DIR=/path/to/fftw3
$ export CMAKE_PREFIX_PATH=/path/to/lapack
```
Note

We just installed LAPACK, so in our case CMAKE_PREFIX_PATH should point to /share/apps/lapack/3.5.0/gcc/5.4.0/

Execute the cmake command with the desired directive destiny.

$ cmake .. -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-ls/4.5.5/gcc/5.4.0/

Execute the make commands sequence.
```
$ make -j <N>
$ make -j <N> install
```

After the installation is completed, you have to create the corresponding module for GROMACS-LS V4.5.5.

#%Module1.0#####################################################################
##
## modulefile /share/apps/modules/gromacs-ls/4.5.5_gcc-5.4.0
## Written by Juan Diego Ocampo & Tomas David Navarro Munera
##

proc ModulesHelp { } {
     global version modroot
          puts stderr "\t Gromacs-ls 4.5.5"
}

module-whatis "(Name________) Gromacs-ls"
module-whatis "(Version_____) 4.5.5"
module-whatis "(Compilers___) gcc-5.4.0"
module-whatis "(System______) x86_64-redhat-linux"

set     topdir            /share/apps/gromacs-ls/4.5.5/gcc/5.4.0
set     version           4.5.5
set     sys               x86_64-redhat-linux

module load fftw/3.3.5_gcc-5.4.0_openmpi-1.8.8-x86_64
module load lapack/3.5.0_gcc-5.4.0

prepend-path      PATH                    $topdir/bin

prepend-path      C_INCLUDE_PATH          $topdir/include
prepend-path      CXX_INCLUDE_PATH        $topdir/include
prepend-path      CPLUS_INCLUDE_PATH      $topdir/include

prepend-path      LD_LIBRARY_PATH         $topdir/lib
prepend-path      LIBRARY_PATH            $topdir/lib
prepend-path      LD_RUN_PATH             $topdir/lib

prepend-path      MANPATH                 $topdir/share/man

References ¶

[1]	GROMACS-LS Documentation. Custom Version of GROMACS. Retrieved May 14, 2020, from https://www.mdstress.org/files/5914/4657/7530/Local_stress.pdf

Authors:

Tomas David Navarro Munera <tdnavarrom@eafit.edu.co>

GROMACS-LS 4.5.5¶

Basic information¶