This tutorial demonstrates creating an MDTraj trajectory from OpenMM data: https://github.com/choderalab/openmm-tutorials/blob/master/01%20-%20Creating%20and%20importing%20molecular%20systems%20in%20OpenMM.ipynb Search for "mdtraj", since it's a ways down. The code for what you want to do will look...

So really what you want to do is build a list of every pair of particles that are within a cutoff distance of each other? That can be done much faster than actually computing all pairwise distances. MDTraj has a `compute_neighborlist()` function that does it pretty quickly. I'd give that a try. Pet...

For what purpose do you want to check the distances? Is it for every pair of particles, or just a subset? How often do you want to do it? There are lots of possible approaches, so I need to know a bit more about what you want to accomplish. Peter This is related to another question of mine https://...

During the simulation I want to check the distance between each pair of particles. I know that I could use state.getPositions to get the positions and then calculate the distance myself, but since openmm must've calculated the distances itself for forcefield, so I'm wondering if I could somehow get ...

If all you want to do is turn off one pairwise interaction, make that one pair an exception. You can initially set the exception parameters to be the same as if it weren't an exception, but then later change its epsilon to 0 (and call updateParametersInContext() to copy it over to the context). On ...

Suppose I have N particles and each pair has a LJ potential. At some point I want to remove the potential defined between particle i and j, but meanwhile leave the potential defined between, say, i and k intact. What is the best way to do this? I guess I could create ~N^2 number of LJ potential obje...

I want to simulate something like a rubberband, applying twisting to which will add up its torsional energy. Basically I want to see the following: Untitled.png The left one is different from the right one because forcing the left one to become a circle will add up its torsional energy. If there is ...

What is the best way to add a torsion rigidity to a worm-like chain in openmm? Specifically, I have a chain of beads connected by harmonic bond, and I want to restrict the rotation of the bonds. One way I can think of is add "side chains" to each of the beads, so that the torsional force field can b...

Thank you very much!

Do you mean that I can do and then and this force is applied to particle 15 instead of 10 after doing these?