From: Chaya Stern (
Date: Fri Mar 20 2015 - 11:11:59 CDT

Take for example cyclooctatetraene. There are alternating single and double
bonds that are not conjugated. Because of symmetry, the bond lengths of the
double bonds and single bonds should be equal (In addition, QM geometry
optimization that I ran also resulted in equal bond lengths for all double
bonds and single bonds. The angles and dihedral are also equal for
symmetrically equal angles and dihedrals). So in this case it would make
sense to force it to be equal during optimization. I can't assign the same
atom type because I still need to differentiate between the single and
double bonds. But when I run the optimization, since I can't force them to
be equal, I get different bond lengths and angle. Some are close enough but
others are significantly different which will result in some asymmetry.

On Fri, Mar 20, 2015 at 11:36 AM, Tim Lo <> wrote:

> Hi,
> If all the parameters related to CD2D1 and CD2D2 are equal, you can simply
> make them to be the same atom type. If this is not the case, do you mean
> that most parameters (e.g. LJ parameters) related to CD2D1 are different
> from those related to CD2D2 while only some parameters (e.g. CD2D1 - CD2D1
> and CD2D2-CD2D2) are the same? Then, be careful as there may be logical
> loopholes. There must be some physical reasons (e.g. experimental evidence)
> to allow you to manually assign most parameters to be the same while some
> parameters are different. Different atom types usually have different
> parameters (except for nonbonded parameters). Manually assigning (or in
> your word, restraining) parameters is not a good way to do parametrization
> (except in some cases where nonbonded parameters are assigned by analogy)--047d7b10cd5382d8300511ba93dd--