Dear LAMMPS users
Is it possible to launch the calculation with the cylindrical particle?
My coarse-grain modelling system is circular polymer molecular ( modeled DNA). I want to implement in the model excluded volume interactions. Excluded volume interactions prevents the situation than granulas overlapping each other in the space and also prevent penetrating the polymeric chain thougt each other. Usually in this case LJ potential (present hard sphere) and FENE-bond potential (doesn’t allow to penetrate chain through each other) is used.
My problem is that my granules-sphere particle presents the peace of polymer have much bigger volume that it should be from the experimental data. If I implement LJ and FENE I will have a problem with whole system volume. I can’t increase the number of particles because my polymer is very huge. The best solution will be the cylindrical particles but I don’t know how to implement it in the LAMMPS.
I will be thankful for any suggestions
Kind regards!
Tatyana Pichugina
Dear LAMMPS users
dear tatyana,
Is it possible to launch the calculation with the cylindrical particle?
My coarse-grain modelling system is circular polymer molecular ( modeled DNA). I want to implement in the model excluded volume interactions. Excluded volume interactions prevents the situation than granulas overlapping each other in the space and also prevent penetrating the polymeric chain thougt each other. Usually in this case LJ potential (present hard sphere) and FENE-bond potential (doesn't allow to penetrate chain through each other) is used.
My problem is that my granules-sphere particle presents the peace of polymer have much bigger volume that it should be from the experimental data. If I implement LJ and FENE I will have a problem with whole system volume. I can't increase the number of particles because my polymer is very huge. The best solution will be the cylindrical particles but I don't know how to implement it in the LAMMPS.
you would have to program a new pair style for that. do you have a
description of the
potential function that you would want to apply? that would be a
starting point. you
can have a look at the code for ellipsoidal particles in the ASPHERE package to
get some inspiration.
I will be thankful for any suggestions
well, using non-spherical particles has its own set of problems, for
example all interactions are dependent
on the relative direction of two particles and that is very time
consuming to compute. also, very long and rigid
cylindrical particles would force you to use a much shorter time step,
so that will not help you so much either.
overall, i don't have a good suggestion, only that what you
propose will have practical difficulties that may outweigh the benefits.
on top of that, it is difficult for me to make practical suggestions
without have some visual "orientation", i.e. some general idea
of what kind of relative shape and property you are looking into.
cheers,
axel.
Tatyana- your problem with maintaining excluded volume is common in soft CG polymers. There are several ways of dealing with it, and one is having cylinders that interact. Like you described, one way could be to use cylinderical particles that store radius/orientation and add a pair_style.
Another way is to use bonds and wrap a nonbond potential around each bond. Then you can experiment with the form of the potential, and make nonbond parameters that keep the chains from crossing. I wrote something like this… it ended up having alot of neighbors for each ‘cylinder’, and the distance between cylinders takes more time to compute than a simple bead-bead distance.
Tim