VMD-L Mailing List
From: Tim Lo (timlo_at_connect.hku.hk)
Date: Fri Mar 20 2015 - 10:36:27 CDT
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).
The University of Hong Kong
On 2015/3/20 下午 10:13, Chaya Stern wrote:
> Is there any way to restrain two bonds or angles or dihedrals to be
> equivalent when I optimize the parameters? For example, if I have two
> bonds, CD2D1 - CD2D1 and CD2D2-CD2D2 and I want them both to have the
> same force constant and equilibrium distance.
> Thank you,
> Chaya D Stern
> Memorial Sloan Kettering Cancer Center
> Tri-Institutional Chemical Biology Program