Documentation

Installing GROMACS-LS (ver. 2016.3)

  • Requirements: FFTW3 compiled with double precision, LAPACK, and CMake

  • Go to the Downloads page and get a copy of the source code.

  • Extract the source code using the tar utility (e.g. tar -xvf gromacs*.tar.gz)

  • Move into the extracted directory and create a new "build" folder (e.g. mkdir build)

  • Move into the build directory and launch ccmake (e.g. ccmake ../)

$> tar -xvf gromacs*.tar.gz
$> cd gromacs*
$> mkdir build
$> ccmake ../

  • Once the ccmake dialog comes up, press c to begin the initial configuration.

  • Modify the CMAKE_INSTALL_PREFIX variable to set the target installation directory. Press g to generate. After ccmake quits, you can follow the standard linux installation commands of make and make install to complete the installation.

$> make
$> make install

 

Supplemental installation instructions and notes

1) By default, GROMACS-LS is compiled in double precision and with optimizations (AVX, GPU, etc.) disabled. Thread-MPI and MPI are also disabled. 

2) If you don’t have CMake installed you can get it here https://cmake.org/download/ 

3) If you don’t have the LAPACK library installed, it is not difficult to compile and install as follows:

$> wget http://www.netlib.org/lapack/lapack-3.5.0.tgz
$> tar -xvf lapack-3.5.0.tgz
$> cd lapack-3.5.0
$> mkdir build 
$> cd build 
$> ccmake ../ 

Once the ccmake dialog comes up, press c to begin the initial configuration. Change the BUILD_SHARED_LIBS flag to ON and modify the CMAKE_INSTALL_PREFIX variable to set the target installation directory. Press g to generate the configuration files and exit ccmake. After ccmake quits, you can follow the standard linux installation commands of make and make install.

4) If you don’t have the FFTW3 library installed in double precission, you can toggle the GMX_BUILD_OWN_FFTW flag to ON to have CMake build it and install it for you during the GROMACS-LS compilation. If you have installed the FFTW3 or LAPACK libraries in a non-standard location (i.e. other than /usr/lib or /usr/local/lib), then before running ccmake you should export the variables FFTW3 ROOT DIR and CMAKE PREFIX PATH, e.g.

$> export FFTW3 ROOT DIR=/path/to/fftw3
$> export CMAKE PREFIX PATH=/path/to/lapack

GROMACS-LS v4.5.5 manual

Local_stress.pdf

 

References

Details of the theory, numerical implementation, and examples: 

  • Vanegas, J. M., Torres-Sanchez, A., and Arroyo, M. Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations. J. Chem. Theory Comput., 10, 691-702. (2014) [Link]
  • Vanegas, J. M. and Arroyo, M. Force Transduction and Lipid Binding in MscL: A Continuum-molecular Approach.  PLoS ONE, 9 (12), e113947. (2014) [Link]
  • Torres-Sanchez, A., Vanegas, J. M., and Arroyo, M. Examining the Mechanical Equilibrium of Microscopic Stresses in Molecular Simulations. Phys. Rev. Lett.  114, 258102 (2015) [Link]
  • Torres-Sanchez, A., Vanegas, J. M., Arroyo, M. Geometric Derivation of the Microscopic Stress: A Covariant Central Force Decomposition. J. Mech. Phys. Solids. 93, 224 - 239 (2016) [Link]

General theory of local stress and central force decomposition:

  • Admal, N. C., and Tadmor, E. B. A Unified Interpretation of Stress in Molecular Systems. J. Elast. 100, 63-143 (2010)
  • Admal, N. C., and Tadmor, E. B. Stress and Heat Flux for Arbitrary Multibody Potentials: A Unified Framework. J. Chem. Phys. 134, 184106 (2011)
  • Tadmor, E. B., and Miller, R. E. Modeling Materials: Continuum, Atomistic and Multiscale Techniques (2011)

Goetz-Lipowsky force decomposition:

  • Goetz, R., and Lipowsky, R. Computer Simulations of Bilayer Membranes: Self-assembly and Interfacial Tension. J. Chem. Phys. 108, 7397-409 (1998)

Virial stress per atom:

  • Thompson, A. P., Plimpton. S. J., Mattson, W. General Formulation of Pressure and Stress Tensor for Arbitrary Many-body Interaction Potentials Under Periodic Boundary Conditions. J. Chem. Phys. 131, 154107-7 (2009)