ok thanks, so the only issue was a change in the default recursion limit setting between 7.3 and 7.4?

thanks,
Jesse

Hi Peter, It looks to me like there's a bug in version 7.4.0/7.4.1 for matching residues that are bonding over periodic images. Code/input files that were working with 7.3 suddenly crash with either 7.4.0/7.4.1 with the error File "/nv/hp22/jmcdaniel43/.conda/envs/openmm74/lib/python3.7/site-package...

Thanks for the quick fix Peter, much appreciated!

Hi all, I'm getting weird energies/simulation results in the special case of simulations with polarizable force fields with the OpenCL kernel running a simulation on 2 GPUs--i think this might be a bug. I'm using OpenMM version 7.2 (cuda 9.0/GTX-1080's but that shouldn't matter...). A similar issue ...

sure, i'll let you know when I'm done with the reference

I think it's doable. If you're computing reciprocal space forces using equation 4.9 in the original PME paper (Essmann JCP 103, 8577, 1995), there's no real difference between taking derivatives of the Q grid w.r.t. cartesian coordinates or a charge scale factor (in fact the latter is easier). And s...

Hi Peter, I need to do thermodynamic integration, and of course need energy derivatives w.r.t. scaling parameters. You've obviously already envisioned this, by enabling methods 'addGlobalParameter' and 'addEnergyParameterDerivative' to most of the force classes, including 'CustomNonbondedForce','Cus...

Hi Peter,

Thanks very much for your time in sorting this out. Much appreciated.

Best,
Jesse

Hi Peter, Yes, I did this with the following code: for i in range(system.getNumForces()): f = system.getForce(i) print(type(f)) f.setForceGroup(i) if type(f) == HarmonicBondForce or type(f) == HarmonicAngleForce or type(f) == PeriodicTorsionForce or type(f) == RBTorsionForce: f.setUsesPeriodicBounda...

Hi all, I am trying to simulate systems that include graphene sheets, which have bonds, angles, and dihedral terms that cross the PBC. According to Fix #1411, this should be implemented in CPU, CUDA, and OpenCL kernels. I am using OpenMM 7.1.1. I find that with CPU kernels, the bonded energy terms o...