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General Discussion
1

Hi Avogardro user
I’m new in Avogadro. I just downloaded it for building input file for GAMESS but I have a problem in $DATA group I can’t make S,P,D.F distribution, can any one help me?

Nagat

2

hi… I’m a new avogadro user.
Can someone tell me if I can use avogadro to observe the hydrogen
bonding in water? I tried placing a few molecules of H2O and enabling
the hydrogen bond display but only a few hydrogen bonds were formed and
I don’t if it that’s accurate.
(choosing options optimize geometry arranges the molecules so that H
bonds are formed but the auto-optimization tool seems to break all those
bonds and arrange the molecules some distance away from each other.)

Is there a way I can visualize the H bond formation in ice?

3

On Thu, Oct 1, 2009 at 12:43 PM, Mahela Munasinghe mahela007@gmail.com wrote:

hi… I’m a new avogadro user.
Can someone tell me if I can use avogadro to observe the hydrogen
bonding in water? I tried placing a few molecules of H2O and enabling
the hydrogen bond display but only a few hydrogen bonds were formed and
I don’t if it that’s accurate.
(choosing options optimize geometry arranges the molecules so that H
bonds are formed but the auto-optimization tool seems to break all those
bonds and arrange the molecules some distance away from each other.)

To get hydrogen bonding geometries, the MMFF94(s) force field is
recommended. Using this force field with the autoopt tool should give
visible hydrogen bonds. You can also play with the hydrogen bond
display type’s settings (distance & angle) to make the criteria less
strict.

Is there a way I can visualize the H bond formation in ice?

You can play around with the autoopt tool to get various arrengements.
However, these minimal energy geometries can’t really be called ice.
They are a collection of H2O molecules in vacuum. To simulate ice, you
could run a molecular dynamics simulation at low temperatures with
periodic boundary conditions. Unfortunally, this isn’t supported in
Avogadro yet.

Hope this helps,
Tim

4

On Oct 1, 2009, at 6:43 AM, Mahela Munasinghe wrote:

the hydrogen bond display but only a few hydrogen bonds were formed
and
I don’t if it that’s accurate.

Please keep in mind that the hydrogen bond display has a few options
– the distance and maximum angle to recognize a hydrogen bond. So if
you change the settings for this display, you will see more or fewer h-
bonds depending on your choices.

(choosing options optimize geometry arranges the molecules so that H
bonds are formed but the auto-optimization tool seems to break all
those
bonds and arrange the molecules some distance away from each other.)

As Tim mentioned, the default for the “Optimize Geometry” is to use
the MMFF94 force field (which explicitly recognizes hydrogen bonds),
while Auto-Optimize defaults to using UFF (which does not, but does
support all elements).

Hope that helps,
-Geoff

5

Hi,

I want to build graphene sheet in Avogadro.
I am able to build a hexagonal cell of the graphene structure. But when I
create a super cell, a message pops out "The document is currently a
isolated molecule. you need to create a unit cell"
Please help me out here.

Thanks

Rajan Kumar
Indian Institute of Technology, Guwahati

6

Hi Rajan,

On Thu, Oct 30, 2014 at 10:07 AM, Rajan Kumar kumarrajan513@gmail.com
wrote:

Hi,

I want to build graphene sheet in Avogadro.
I am able to build a hexagonal cell of the graphene structure. But when I
create a super cell, a message pops out “The document is currently a
isolated molecule. you need to create a unit cell”

Use Crystallography >> Add Unit Cell and adjust the cell parameters to
match your desired periodicity. After that, you should be able to produce a
supercell.

Hope this helps,
Dave

7

Use Crystallography >> Add Unit Cell and adjust the cell parameters to match your desired periodicity. After that, you should be able to produce a supercell.

Or, you can start with graphite:

There are a few ways to do this. Probably the easiest would be to open up the crystal structure of graphite:

Then in the dialog, pick out the graphite unit cell:

Then generate a larger “super cell” as needed:

I’d recommend something like A x5, Bx5. Then you’ll have dual-layer graphene and you can select and remove the bottom layer.

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com mailto:geoffh@pitt.edu
web: http://hutchison.chem.pitt.edu/ http://hutchison.chem.pitt.edu/

8

Hi,
I am trying to build graphene using Avogadro. I tried the following steps:

  1. Draw six carbon with alternate single and double bonds.
  2. Optimize geometry.
  3. Add unit cell
  4. Build super cell

As a final structure, I got carbon molecules randomly connected to each
other.
Please help me where I am wrong.

Thanks
Rajan Kumar

9

Did you adjust the unit cell dimensions to match your desired periodicity?
If not, you won’t get a meaningful structure out.

See Geoff’s suggestion about importing the crystal. That method should have
the unit cell preconfigured to what you’re looking for.

On Thu, Oct 30, 2014 at 3:59 PM, Rajan Kumar kumarrajan513@gmail.com
wrote:

Hi,
I am trying to build graphene using Avogadro. I tried the following steps:

  1. Draw six carbon with alternate single and double bonds.
  2. Optimize geometry.
  3. Add unit cell
  4. Build super cell

As a final structure, I got carbon molecules randomly connected to each
other.
Please help me where I am wrong.

Thanks
Rajan Kumar

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