Hello Guys,
I have a question. Does lammps have the capability of representing a molecular chain with geometrical elements. For instance, cylindrical elements and not just point masses. If it is possible, how can it be done. Finally, is it possible to employ a potential that is a function of 2 variables and not just the distance between the two particles. For instance, a potential that is a function of distance and the orientation angle of the chain.
Thanks
Hello Guys,
I have a question. Does lammps have the capability of representing a molecular chain with geometrical elements. For instance, cylindrical elements and not just point masses. If it is possible, how can it be done.
all features, that LAMMPS possesses are described in the manual. if
the feature you are looking for is not described in the manual, you
can safely assume, that it is not (yet) available.
doing a cylinder in an classical MD code is *very* tricky, as any
objects with hard edges are. the closest are the ellipsoids in ASPHERE
package. mind you there orientation dependent potentials are quit
expensive compared to simple (soft) point particles.
i recall some work by carolyn phillips when she was working in the
group of sharon glotzer, where they came up with a scheme to build
shaped objects (i.e. tetrahedra) from a superposition of polydisperse
point particles. if you write a tool that would generate such objects
out to a data file and then use a rigid body integrator, you would be
able to run this in LAMMPS.
Finally, is it possible to employ a potential that is a function of 2 variables and not just the distance between the two particles. For instance, a potential that is a function of distance and the orientation angle of the chain.
difficult to say. as before, if you can map it to a superposition of
existing functionality, you may just need a smart way to generate your
input, otherwise, you may be required to add new styles to LAMMPS.
axel.
You can overlap spheroid (finite diameter) particles
to get a good approximation to an ellipsoid
and treat each clump of particles as a rigid body.
People do that often for granular systems.
There are various colloidal potentials in LAMMPS
that operate with finite-size particles. They
operate pairwise bewteen pairs of spheroids,
but with the rigid body constraints, they would
have an effective orientational dependence.
Steve