Constraints

General Discussion
1

Good Afternoon

I am using the first version of Avagadro. I am trying to optimize
geometry while preserving certain angles. I know it is possible to
constrain specific positions, or to ignore certain atoms entirely.

When I go to Extensions-> Molecular Mechanics-> Constraints… menu, I
specify torsional angle, then input the specified angle and atomic
indices. The index choices allow only numeric input, so I am not sure
how the program differs between, for example, C1 or H1, for an input of

  1. I assume it might consider spacial arrangements and then locate the
    closest atom compared to other indices prescribed. When then selecting
    UFF (or any force field), the relaxation does not constrain the
    specified requirements.

Moreover, when going to View->Properties->Torsion Properties…, I set
the angles as close to desired angle as possible (changing one angle
affects another). This still does not force the set constraints to hold.

When using other constraints like fix atom, the application works, but
has severe consequences in molecular geometry producing chemically false
geometries.

Could you please provide me with a process to either

a.) keep a specific symmetry of a molecule constant

or

b.) set torsional angles to specific quantity and keep them constant
without constraining the atoms specific position.

Thanks

–
Thanks for your time,

Gregory Theophall
Rensselaer Polytechnic Institute
110 8th St
Troy, NY 12180

2

Hello,

To set the constraint you need to know the atom id number.

In the Display Settings window select the Label option. You may also want to click on the wrench symbol for Label an make sure that the Atom Label text is set to “Atom number” which is what the constraints dialog is expecting.

Make sure that you click “Add” after setting the constraint.

You might also have to close the Constraints dialog before it will let you optimize the geometry after setting the constrain.

I’m not sure if you can set the geometry using Avogadro.

Hope this helps,

Steve

Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657
swathen@sienaheights.edu

From: theopg [theopg@rpi.edu]
Sent: Tuesday, June 23, 2015 3:02 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Constraints

Good Afternoon

I am using the first version of Avagadro. I am trying to optimize
geometry while preserving certain angles. I know it is possible to
constrain specific positions, or to ignore certain atoms entirely.

When I go to Extensions-> Molecular Mechanics-> Constraints… menu, I
specify torsional angle, then input the specified angle and atomic
indices. The index choices allow only numeric input, so I am not sure
how the program differs between, for example, C1 or H1, for an input of

  1. I assume it might consider spacial arrangements and then locate the
    closest atom compared to other indices prescribed. When then selecting
    UFF (or any force field), the relaxation does not constrain the
    specified requirements.

Moreover, when going to View->Properties->Torsion Properties…, I set
the angles as close to desired angle as possible (changing one angle
affects another). This still does not force the set constraints to hold.

When using other constraints like fix atom, the application works, but
has severe consequences in molecular geometry producing chemically false
geometries.

Could you please provide me with a process to either

a.) keep a specific symmetry of a molecule constant

or

b.) set torsional angles to specific quantity and keep them constant
without constraining the atoms specific position.

Thanks

–
Thanks for your time,

Gregory Theophall
Rensselaer Polytechnic Institute
110 8th St
Troy, NY 12180

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