OK thanks.

The simulation qualitatively looks OK, nothing bizarre happening.

Hi All, I'm getting a user warning about non-optimal GB parameters when trying to run an implicit solvent simulation from LEaP inputs. Based on the code generating the warning this is because of an apparent mismatch between the radii and the screening terms. Specifically, I'm selecting the "GBn2" mo...

Hi, I'm wondering if it is possible to use the Multiple timestep integrator to evaluate forces outside the nonbondedCutoff less frequently than the other forces? Since the identity of forces outside this cutoff would change over time, it seems the forcegroups would have to be updated every X timeste...

OK perfect, thanks for the reply!

I'm keen on using the multiple timestep integrator, but with constant temperature. What is the best way to go about this? Typically I would just use the Langevin integrator to do both integration and thermal control, but writing a custom integrator that combines rRESPA with Langevin by using the The...

Oh nice, I was having exactly the same problem and my current workout was to pre-translate all my starting structures. I'll test this out. One thing to note, the internal translation that OpenMM applies only seems to occur DURING the simulation. If you ask for the particle positions after simulating...

I see, good to get to the bottom of it, and understand why it required some dynamics to see the problem.

Ok, I'm interested to know what is actually happening with the forces. I've attached a zip of the relevant files, so you can just run AngleTestCase.py In the restraint string generating function I've left it as -1 and 1, which should fail with NaN errors. I've put the -0.99 and 0.99 lines commented ...

Peter, So I was re-writing the code to have something nice and clean to send you, when I realized a potential logic flaw in that the min/max nest I'd used for the angles looked like this: angle1 = 'acos(min(max(' + cosine + ', -1), 1))' and a similar thing for the asin portion. But, of course we don...

I had a go at trying to isolate the problem, there are some odd things: First, I tried my expression with just a 3 atom system with no bonds, and it works well under all conditions. In fact, just using the acos method even seems to be stable at 180 degress Second, I moved to a 3 water system, using ...