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
- 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
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
Could you please provide me with a process to either
a.) keep a specific symmetry of a molecule constant
b.) set torsional angles to specific quantity and keep them constant
without constraining the atoms specific position.
Thanks for your time,
Rensselaer Polytechnic Institute
110 8th St
Troy, NY 12180