[gmx-users] The octahedron problem

[Barnett, James W]

>I have the problem with generating the octahedron box.  I always get the
rectangular box (using VMD)

That's normal and not a problem:

"any periodic cell shape can be expressed as a parallelepiped (a.k.a. triclinic cell), and GROMACS does so internally regardless of the initial shape of the box."
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions



--
James "Wes" Barnett
Ph.D. Candidate
Chemical and Biomolecular Engineering

Tulane University
Boggs Center for Energy and Biotechnology, Room 341-B
New Orleans, Louisiana 70118
jbarnet4 at tulane.edu​
LinkedIn​​


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Vy Phan <phanvy120690 at gmail.com>
Sent: Tuesday, May 19, 2015 6:18 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] The octahedron problem

Dear Gromacs Users,
I have the problem with generating the octahedron box.  I always get the
rectangular box (using VMD)
When I searched on the gmx maillist, I saw some people met same problem.
Is problem is normal in gromacs?

After run simulation, I can display the trajectory on VMD by using the
command trjconv -pbc mol -ur compact for converting the system. But I can
not display the octahedron box after solvated system.

Could someone help me ?

Tuong Vy
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