Just to elaborate, this would be kind of like your method 1. Build your list normally Create your custom non-bonded force object Loop over all particles Copy the parameters from the old non-bonded force object to your custom one Set lambda appropriately for each particle Remove the old non-bonded fo...

Hi Mark,

Why not make lambda a per-particle parameter? Then you replace the existing non-bonded function with this one and set lambda to zero for the particles that have the normal interactions.

Justin

Take a look at the developer guide, and ask as many questions as you want. And yes, it would be helpful if we had a minimal example plugin to start from. AMOEBA and RPMD can be used as examples, but they're more complicated. Perhaps we can create that soon. Peter, thanks again for your help! I've s...

Hi Peter, I assmed the existing kernels wouldn't break this up per bond. Is there anyway to squeeze that functionality into a new kernel that still sits in the rest of the openmm framework? We currently calculate all of these per bond energies on the CPU, but it's very slow because we have large num...

Is there any way to get per-bond energies out of the kernels and into the State objects? For example, I might add a HarmonicBondForce to the system and then add many bonds. For our particular application, it is necessary to get the energies of the individual bonds. Is that possible using the existin...

OK, the CustomCompoundBondForce route is not going to work. I wrote a simple test with #I = #J = 20 and then added a single restraint of this type to the system. Setting up the system takes ~10-15 minutes, which is presumably due to evaluating the complicated expression and taking derivatives of 40 ...

Peter, Thanks for the input. There are many helpful ideas there. I will probably try my approach, just to see what happens. Possibly using your padding approach to reduce the number of unique forces. Ultimately, writing a plugin is probably the most sensible way forward. I just don't want to :) . I ...

Could you explain more about what you're doing? What are you using this potential to model? When you say, "the number of I's and J's will change," do you mean during a single simulation, or between different simulations? Also, am I correct in understanding that the constraints are not based on the ...

I am interested in adding r^-6 weighted distance restraints. In these calculations, you have two groups of atoms, I and J, and you compute an energy based on the r^-6 average of all of the pairwise distances between the I's and J's: E = 0.5 * k * (r_eff - r_0)^2 r_eff = ( sum_ij(r_ij^-6) / N ) ^ (-1...

All of the tests pass except: ./TestCudaCustomGBForce exception: Assertion failure at TestCudaCustomGBForce.cpp:253. Expected 6568.5, found 6696.99 The failure is in testMembrane, if I comment out this test, then everything passes. Should I be concerned?