[gmx-users] Resources on simulation walls
francesco.oteri at gmail.com
Sat Mar 10 18:53:37 CET 2012
at http://manual.gromacs.org/online/mdp_opt.html#nl the manual says:
"Without walls or with only one wall the system size is infinite in the
z direction. Therefore pressure coupling or Ewald summation methods can
not be used. These disadvantages do not apply when two walls are used"
So I guess wall are physical walls, i.e. something limitating the
expansion of your system in the z-direction. In the xy plane the system
is replicated because of pbc but,
without walls, it would be unlimited in the z-direction.
Il 10/03/2012 17:46, Andrew DeYoung ha scritto:
> Only if you have time, do you know of any resources that explain the concept
> of a Gromacs wall, which seems related to 2-D Ewald summation? In the
> Gromacs 4.5.4 manual, the parameters related to walls are described on page
> 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls
> . But do you know of any general explanations, books, or literature papers
> that would help me to understand what a wall does and why and when I need to
> use them? I cannot seem to find them discussed in the main Gromacs papers (
> http://www.gromacs.org/Documentation/Gromacs_papers ).
> Also, is there another name for a simulation wall? When I use Google to
> search for "MD simulation wall", it is not clear that I am looking for the
> correct thing.
> Thanks so much for your time.
> Andrew DeYoung
> Carnegie Mellon University
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