Dear Peter,

That makes sense to me! Thank you so much for your help!!

Best,
Xinyu

Dear Peter, This clarification is very helpful to me. Many thanks! By the way, I have another question about the Periodicity of Bond Forces. I have a CustomBondForce which is used for calculating a collective variable between two diffenent molecules. Then I used that collective variable as a reactio...

Dear Peter, Thank you very much for your reply. And yes, your understanding is correct. I know it's complicated and I have no idea about how to compute the transformation matrix in an openmm force field - I didn't find a way to read the coordinates of a whole structure during openmm simulation. I wa...

Dear Peter, Thank you so much for your quick reply. I'd love to use mdtraj but I'm wondering how to use it in a force field function - I'm writing a cartesian principal component biased potential, like V=k*(pc-pc0)^2. But I need to superpose structures when computing "pc" for each structure during t...

Dear all, Hope you all are doing well! I'm wondering if there is a way to superpose structures first before calculating a specific potential. I have a reference structure and I'd like to superpose structures to it and then use the superposed coordinates to calculate a certain potential. Your helps a...

Thank you so much for your quick reply! It's pretty helpful!

Dear OpenMM developers: I'm setting up a simulation with PBC, and find that there are two functions for defining the periodic box: topology.setPeriodicBoxVectors() and system.setDefaultPeriodicBoxVectors(). I'm wondering which one should be chosen and what's their differences? I'll really appreciate...