[gmx-users] Box shape changing from rectangle to parallelogram at NVT

[Marlon Sidore]

Hello,

I am trying to set up a DAFT approach for membrane segments using MARTINI (
http://www.cgmartini.nl/index.php/329-the-daft-approach-to-membrane-protein-assembly)
and I've made simulation boxes as small as in the original paper.
However, I'm not sure if everything is fine or not: the shape of the box
changes from a rectangle to a parallelogram (see pictures).
Since I've never seen that, I'm wondering if that's a problem - boundary
conditions don't seem problematic (no holes when vizualizing them with
VMD), but still I doubt.

I am linking to my drive since eduroam won't let me use another image
hosting site:
https://drive.google.com/open?id=1PKtivk4lSygMgWey-N5PGhwGZ3JQJJw_

Best regards,

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France