Wrote a working 50-line pytorch protein molecular dynamics engine in numpy autograd which I am now porting to pytorch

Here’s the code:

```
!pip install autograd
!pip install celluloid
import matplotlib.pyplot as plt
import numpy as np
import torch
n_molecules = 50
n_atoms_per_molecule = 2
box_size = 20
temperature = 0.5
def energy(positions):
"Compute the energy of a Lennard-Jones system."
sigma = 1.0
epsilon = 1.0
rc = 3 * sigma
e0 = 4 * epsilon * ((sigma / rc)**12 - (sigma / rc)**6)
natoms = positions.shape[0]
a, b = torch.triu_indices(natoms, natoms, 1)
d = positions[a] - positions[b]
r2 = torch.sum(d**2, dim=1)
c6 = (sigma**2 / r2)**3
energy = -e0 * (c6 != 0.0).sum()
c12 = c6**2
energy += torch.sum(4 * epsilon * (c12 - c6))
return energy
def total_energy(positions):
return energy(positions)
velocities = torch.tensor(np.random.uniform(low=-10, high=10, size = (n_molecules, 2)), requires_grad=True)
positions = torch.tensor(np.random.uniform(low=-box_size/2, high=box_size/2, size = (n_molecules, 2)), requires_grad=True)
from celluloid import Camera
camera = Camera(plt.figure())
for t in range(10000):
energies = total_energy(positions)
energies.backward()
with torch.no_grad():
forces = -positions.grad
velocities = velocities +forces*1e-2
#velocities = velocities * torch.sqrt(temperature/ torch.mean(velocities**2)) #thermostat
positions= positions + velocities*1e-2
anim = camera.animate(blit=True, interval=50)
plt.style.use("dark_background")
anim.save('output.mp4')
```

However I get an error of

`RuntimeError: element 0 of tensors does not require grad and does not have a grad_fn`