Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Pawel <>
Date: Wed, 13 Nov 2013 08:07:43 -0500

Hi Thomas,

Just o clarify this and your follow up question: I would be worried
about those gaps. To me it looks like somehow your periodic box does not
correspond to the box that was used to solvate the molecule. As said
before, if you'd like to simulate a hexagonal system it's as simple as
creating a triclinic cell with a a c 90 90 120 cell parameters. In NAMD
you need to transform that into the cartesian basis and feed those
values to the cellBasisVector cards.

One other idea: if I understand correctly that system you showed was set
up with NAMD. Why not set up a hexagonal system with Amber and compare?
If done correctly they should look the same.


On 11/12/2013 04:11 PM, Thomas Evangelidis wrote:
> Is it because I start from a hexagonal prism box generated by CHARMM-GUI?
> >How did you generate the triclinic box you showed? It looks like a hexagon
> >before wrapping (or "imaging" in AMBER language) water coordinates to the
> >central cell.
> >
> >thanks,
> >Thomas

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Received on Wed Nov 13 2013 - 05:30:04 PST
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