Hello, dear Avogadro community!
I use Avogadro since a few years, so I’d like not to change it. But at
the moment I have to model my systems using some simple MM, even maybe
sort of Lennard-Jones-potential code (adsoption by non-polar functional
groups on porous coordination polymers) due to large size of them. I
tried to apply Avogadro to this problem, as it is free and implements
UFF potential. But at the moment I tried to constraint some internal
coordinates and found that maximum distance between atoms to be
constrained is 5.0 A. Are there any reasons for this limitation and are
there any ways to bypass it? In fact I try to simulate some sort of
surface scans directing a substrate molecule along the directions of
interest — maybe there are more appropriate ways to do this that I’ve
missed?
Thanks in advance!
Anton S. Lytvynenko,
L. V. Pisarzhevskii Institute of Physical Chemistry of the National
Academy of Sciences of the Ukraine.