Re: NAMD octahedron

From: Sterling Paramore (
Date: Thu Mar 09 2006 - 10:44:56 CST

I found the gromacs user manual helpfull for this (search for

Truncated octahedron periodic boundary conditions are isomorphic to
parallelepiped boundary conditions with specific cell vectors. So just
pick a minimum image distance, d, and use the vectors described in the
gromacs manual to set the cellBasisVector matrix. If you view the
simulation in VMD, it will look like a parallelepiped and not a
truncated octahedron, but they have exactly the same properties, so it
doesn't matter.

You shouldn't need to change the pressure control settings, or anything
about the force field. You most certainly do NOT want to useFlexibleCell
or useConstantRatio (it would likely ruin the truncated octahedron).

If you want to run NVT, just don't use a piston.


matteo filandri wrote:

> Dear all,
> Before it possible to build this type of PCB with
> NAMD???
> 1. If yes how can I do this and how do I set the "cellBasisVector"
> matrix????
> 2. Is it necessary to setting the pressure control with different
> values than,
> for example, GramicidinA tutorial???
> 3. Can I use the parm7 and inpcrd files of AMBER with truncated
> octahedron PCB
> system with NAMD???
> 4. I need to run a NVT dynamic before an NPT one. Can I use the
> settings wrote
> in the GramicidinA tutorial, where the dimensions of the box are free
> to move??
> useGroupPressure yes # smaller fluctuations
> useFlexibleCell yes # allow dimensions to fluctuate
> independently
> useConstantRatio yes # fix shape in x-y plane
> 5. or can you give me some infos about setting an NVT dynamic with NAMD??
> Thank you in advance and have a good day.
> _________________________________________________________________
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