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.