Software

GROMACS-LS and MDStress library

GROMACS-LS and the MDStress library enable the calculation of local stress fields from molecular dynamics simulations.

You can download the latest version of the code here:

gromacs-ls-2016.3-12282019.tar.gz (bundled version that includes mdstress-library)

mdstress-library-12282019.tar.gz (standalone library)

Note that the mdstress.org website is broken at the moment :'-[

Installing GROMACS-LS (ver. 2016.3)

Requirements: FFTW3 compiled with double precision, LAPACK, and CMake
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
By default, GROMACS-LS is compiled in double precision and with optimizations (AVX, GPU, etc.) disabled. Thread-MPI and MPI are also disabled.
If you don’t have CMake installed you can get it here https://cmake.org/download
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.
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 source code and manual

gromacs-4.5.5-ls-5.0.tar.gz

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)

Software

GROMACS-LS and MDStress library

You can download the latest version of the code here:

Installing GROMACS-LS (ver. 2016.3)

GROMACS-LS v4.5.5 source code and manual

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