2 questions about optimization

General Discussion
1

Hi all,

Sorry, I will put two questions in one email:

  1. In the Avogadro’s autooptimization tool the phrase “fixed atoms are movable” is ambiguous. Does it mean “selected atoms are movable”?

  2. I’ve read that Dreiding atom types already are determined by openbabel. Will the Dreiding optimization be introduced into Avogadro any time in the future?

Best regards,

Vis

2
  1. In the Avogadro’s autooptimization tool the phrase “fixed atoms are movable” is ambiguous. Does it mean “selected atoms are movable”?

There’s a concept of a “fixed atom” (i.e., not affected by optimization – frozen in space). Maybe “frozen” is a better word.

The option means that you can manually move these fixed atoms.

If anyone has a better idea for wording, we’re always open to them!

  1. I’ve read that Dreiding atom types already are determined by openbabel. Will the Dreiding optimization be introduced into Avogadro any time in the future?

Maybe. Right now, I think our main interest is improving optimization speed. But if there’s interest in Dreiding, please let me know or add it as a feature request!

Thanks very much,
-Geoff

3

Hi people.

I have a similar question.

does exist a project to open and manipulate amber files (for example) in
Avogadro? I mean, we have nice Force fields to work with small
molecules but we don’t have a force field to macromolecules.

Thks

2011/4/20 Geoffrey Hutchison geoff.hutchison@gmail.com

  1. In the Avogadro’s autooptimization tool the phrase “fixed atoms are
    movable” is ambiguous. Does it mean “selected atoms are movable”?

There’s a concept of a “fixed atom” (i.e., not affected by optimization –
frozen in space). Maybe “frozen” is a better word.

The option means that you can manually move these fixed atoms.

If anyone has a better idea for wording, we’re always open to them!

  1. I’ve read that Dreiding atom types already are determined by
    openbabel. Will the Dreiding optimization be introduced into Avogadro any
    time in the future?

Maybe. Right now, I think our main interest is improving optimization
speed. But if there’s interest in Dreiding, please let me know or add it as
a feature request!

Thanks very much,
-Geoff

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