Alex Berlaga

Gyration tensor, principal moments, and asphericity over PBCs

1

Hi, I am interested in calculating the gyration tensor, principal moments, and asphericity of a cluster of molecules over time. At certain points, some molecules cross a periodic boundary, and...

Particle Coordinate is NaN occasionally upon molecule hitting PBCs

5

I am running large numbers of simulations of three peptide-like molecules in water (starting in a triple-helical conformation). In my simulations, I increase the temperature every by 1 K/nanosecond. In...

Transparent shapes

2

Is there a way to make an added shape have some transparency? I tried changing the color to a 4-element list, but that didn't work: ``` view.shape.add_sphere(zcc_point * 10, [1,...

PYTORCH_MODEL with CUDA 11.2

2

Dear Plumed Team, I am using PLUMED 2.10b with CUDA 11.2 and I am attempting to enable libtorch to use the Pytorch module. I have tried with multiple versions of...