GROMACS-LS manual: Local_stress.pdf

MDStressLib manual: Coming soon...


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. DOI: 10.1016/j.jmps.2016.03.006 (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)