How to draw a plane

is it possible to draw a plane and mount molecule on it, to simulate the
deposition of a film on a substrate?

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562


http://www.linkedin.com/in/claudiubucur

is it possible to draw a plane and mount molecule on it, to simulate the deposition of a film on a substrate?

No, not really. The first part of that “draw a plane” is the sticking point. It is possible to align molecules in particular planes and/or simulate depositing molecules on a substrate.

To align a molecule, use the Align tool:
http://avogadro.openmolecules.net/wiki/Align_Tool

Hope that helps,
-Geoff

thank you,
i was able to allign my polymer chains to a plane and then use gimp to
“mount” that layer on top of a “substrate” layer and get an image of an
“adsorbed” film.

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562


http://www.linkedin.com/in/claudiubucur

On Mon, Jun 28, 2010 at 3:01 PM, Geoffrey Hutchison <
geoff.hutchison@gmail.com> wrote:

is it possible to draw a plane and mount molecule on it, to simulate the
deposition of a film on a substrate?

No, not really. The first part of that “draw a plane” is the sticking
point. It is possible to align molecules in particular planes and/or
simulate depositing molecules on a substrate.

To align a molecule, use the Align tool:
http://avogadro.openmolecules.net/wiki/Align_Tool

Hope that helps,
-Geoff


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Claudiu,

How did you use the align tool to do that? - it seems that it can only
align one molecule at a time to a particular axis. It seems quite
difficult to me to align more than one molecule to a plane.

Thanks,

Phil.

On 2010-07-30 01:26, Claudiu Bucur wrote:

thank you,
i was able to allign my polymer chains to a plane and then use gimp to
"mount" that layer on top of a “substrate” layer and get an image of an
"adsorbed" film.

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562
www.claudiubucur.com http://www.claudiubucur.com
http://www.linkedin.com/in/claudiubucur

On Mon, Jun 28, 2010 at 3:01 PM, Geoffrey Hutchison
<geoff.hutchison@gmail.com mailto:geoff@geoffhutchison.net> wrote:

 > is it possible to draw a plane and mount molecule on it, to
simulate the deposition of a film on a substrate?

No, not really. The first part of that "draw a plane" is the
sticking point. It *is* possible to align molecules in particular
planes and/or simulate depositing molecules on a substrate.

To align a molecule, use the Align tool:
http://avogadro.openmolecules.net/wiki/Align_Tool

Hope that helps,
-Geoff


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Australia
E-mail: phil@pricom.com.au