Sukrit Singh
Sukrit Singh
Oh! I didn't realize that the two CLIs allowed for different YAMLs - this is what I was looking for. Thanks so much for that example, @zhang-ivy! Future integrating of...
Oh – I wasn't aware that Plugin existed at all! I've managed to install it and it accepts the `PlumedForce` for both a distance and a torsion with no complaints...
Just wanted to update: the [PLUMED plugin](https://github.com/openmm/openmm-plumed/) works perfectly for this purpose! For posterity – I've written a minimal example below (using the same original files attached above) that accepts...
After discussing with @jchodera we decided to try and see what happens if we run `Metadynamics` objects with the distance variable set to `periodic=True`. The initial script looks something like:...
Sure thing! This is for when the `periodic=True` setting is used for the distances. ``` --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Input In [51], in () 1 # the...
Oh! I moved any `bias.npy` files in the directory to a tmp folder (older versions from other tests), and it worked! I was under the assumption that `Metadynamics` objects write...
Ah thanks for pointing that out! Totally missed that bit in the docs when I was going through them. One bizarre thing I'm noticing is when I run a metadynamics...
Sure. Documented below: Commands used to create and setup a dev-env: ``` conda create --name dev-openmm python=3.9 OPENMM_CUDA_COMPILER=/usr/bin/nvcc conda install -c omnia-dev/label/cuda113 -c conda-forge openmm ``` Re-ran using the same...
Ohhhh yes these are all with `frequency=1` and `saveFrequency=10` – I didn't realize that the values were too frequent for the disk-writing operation! Would having `frequency=50` still be too low?...
Finally getting a chance to revisit this. Sorry for the delay – Been dealing with a broken arm. Below is a plot of the speed (ns/day) of the system at...