Hi ! I'm back because the code "works" in that it succesfully generates a simulation, but the results make no sense. so the idea is to calculate Hydration energy of Glycine with an alchemical method, where the interactions between Glycine and the rest of the system are scaled by a factor of lambda g...

ok, I must've set an exception in the first itteration of the code and then missunderstood the API.

I don't know why this code previously brought up the exceptions error, I guess I didn't comment a line I should've or something stupid...

thanks a lot for the help !

ok but here I exclude the residue atoms from the nonBondedForce by doing nonbonded_force.setParticleParameters(i, 0, 0, 0) #remove target atoms from the nonbonded force for i in the target molecule. If I then do what you suggest, aren't I also going to exclude those from the CustomNonBondedForce tha...

Hi ! I gave it a few days to see if I got a response from the github and no so here goes. I started off trying to create a scalable custom non bonded force for the residue I want to solvate, and creating an exception in the default nonbonded force for the residue's atoms. I got an "forces must have ...

Will do, thanks ! If that doesn't work, is there a way to do that directly through base openmm tools ? I'd tried using a custom-force to treat part of the system but got an error where exceptions in the non-bonded force and customnonbonded force had to be the same, even if I just used exclusions sho...

Hi all, hopefully this is the right place to ask about this, I'm trying to understand how to use the openmm-tools library to do TI and solvate a glycine in water, but as soon as lambda is slightly low (0.8) the glycine coordinate explode all over the place. I seems like all intra-molecular forces ar...