Project

General

Profile

Feature #2643

mdp options and/or docs for anisotropic aspects of implementations

Added by Mark Abraham 12 months ago. Updated 12 months ago.

Status:
New
Priority:
Low
Assignee:
-
Category:
core library
Target version:
-
Difficulty:
uncategorized
Close

Description

By long convention, GROMACS expects membranes to be oriented so that the Z-axis is the surface normal. We have some other places of more-or-less surprising anisotropy (DD decomposition works best if the x and y dimensions are not much longer than the z dimension, some analysis tools partition the cell into boxes along axes).

At https://gerrit.gromacs.org/#/c/8314/3/src/gromacs/mdlib/mdebin.cpp we thought perhaps an .mdp option that declares this could be useful, although for now we would only implement e.g. the z option. At least then it is easier for the user to see that their choices are not free.

History

#1 Updated by Mark Abraham 12 months ago

  • Category set to core library
  • Priority changed from Normal to Low

#2 Updated by Berk Hess 12 months ago

An mdp option could be Z by default, but also have options X, Y and none.

Also available in: Atom PDF