Re: AMBER: Conversion between truncated octahedron and orthorohombic box

From: Gustavo Seabra <>
Date: Mon, 27 Oct 2008 13:19:59 -0400

On Sat, Oct 25, 2008 at 10:36 PM, #NGUYEN CONG TRI# wrote:
> Dear all,
> I pre-equilibrated my system in Amber in a very long simulation. To reduce
> the box size I used a truncated octahedron box. I'd like to use that
> equilibrated structure for a QM/MM simulation with Gromos Interface. So I
> have to convert the coordinate and topology into Gromos format. But I wasn't
> aware that only orthrhombic box is allowed.
> Is there anyway to convert the truncated octahedron into
> orthorhombic symmetry without having to equilbrate my system again?

As Ross suggested, even if it's possible you will probably have to run
some sort of extra equilibration with your system. That leads me to a
different suggestion: unless there is a special reason why you want to
use Gromos, why not just use Amber for the QM/MM calculations?

Also, notice that when you change to a QM/MM Hamiltonian,
independently of what program you use, you will still need some
re-equilibration - a system that is relaxed on a MM Hamiltonian is not
necessarily relaxed for the QM one. As you change Hamiltonians, you
need to give the system some time to relax.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Oct 29 2008 - 05:08:02 PDT
Custom Search