VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Mar 20 2015 - 12:04:04 CDT

Indeed there are some very clear examples where this type of constraint is desirable; however, it will require non-trivial modification of the optimization code and interface. As I said previously, it's on our TODO list, but unfortunately it's not a feature that we can offer at this time.

Regards,
Christopher Mayne

On Mar 20, 2015, at 11:11 AM, Chaya Stern wrote:

> 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 <timlo_at_connect.hku.hk> 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)