Small Update to GROMACS-LS and MDStress Library
Posted by admin on December 28, 2019
Added a new option to gmx_LS mdrun to improve analysis of certain simulation trajectories. The new option: -lsmindihang <real> (0) allows users to not include dihedral local stress contributions if the angle is very close to a planar configuration (determined by the sin(|phi|)). Use this flag if there is a dihedral potential (e.g. CHARMM36 lipid FF) that has been parametrized with a min/max that is not 0/Pi and the stress profiles show large noise that does not converge with additional frames. A -lsmindihang value of 0.0005 is typically sufficient to fix this problem. Also added the option to translate local stress files using pbc along any dimension using the tensortools flag --trans. This option can only translate the stress grid by integer grid displacements. Visit our Downloads page to get the latest version.
New beta version of GROMACS-LS available for testing
Posted by admin on February 23, 2019
A new beta version of GROMACS-LS based on version 2016.3 is available for testing. Please visit the Downloads page to get the new source code.
Fixed small error in nonbonded kernels
Posted by admin on May 17, 2016
A small error was fixed in the local stress indexing of two of the nonbonded kernels used to calculate the TIP4P water interactions (nb_kernel104.c and nb_kernel133.c). This bug only affected analysis of simulations with TIP4P water molecules. The latest version of the code is available in the Downloads section or through bitbucket.
New paper in press!
Posted by admin on March 11, 2016
Our new paper "Geometric derivation of the microscopic stress: A covariant central force decomposition" is now in press at the Journal of the Mechanics and Physics of Solids. You can find it at the following url: http://dx.doi.org/10.1016/j.jmps.2016.03.006
MDStress.org is live!
Posted by admin on July 22, 2015
The web is up!