Problem in make_deltaforces() of Chignolin_Coarse-Grained_Tutorial.ipynb

[a96123155]

Hi, there is a problem in Chignolin_Coarse-Grained_Tutorial.ipynb:

>>> make_deltaforces(coords_npz, forces_npz, delta_forces_npz, forcefield, psf, exclusions, device, forceterms) Check for broken coords. 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:00<00:00, 985.43it/s] No broken frames /home/ubuntu/.local/lib/python3.9/site-packages/torchmd/systems.py:49: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor). self.pos[:] = torch.tensor( /home/ubuntu/.local/lib/python3.9/site-packages/torchmd/systems.py:73: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor). self.box[r][torch.eye(3).bool()] = torch.tensor( Producing delta forces 0%| | 0/18689 [00:00<?, ?it/s] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/ubuntu/.local/lib/python3.9/site-packages/torchmd_cg/utils/make_deltaforces.py", line 80, in make_deltaforces Epot = forces.compute(co.reshape([1, natoms, 3]), system.box, system.forces) File "/home/ubuntu/.local/lib/python3.9/site-packages/torchmd/forces.py", line 293, in compute E, force_coeff = evaluate_repulsion_CG( File "/home/ubuntu/.local/lib/python3.9/site-packages/torchmd/forces.py", line 429, in evaluate_repulsion_CG coef = B[atomtype_indices[:, 0], atomtype_indices[:, 1]] TypeError: 'NoneType' object is not subscriptable

[Lord-Kelsier]

Hey @a96123155, I manage to fix it by adding Lennard-Jones potential in the force terms: forceterms = ['Bonds','RepulsionCG', "lj"].

That's because 'RepulsionCG' requires the B term of the LJ potential ( $4\varepsilon (\frac{\sigma}{r}) ^ 6$ )

[ARKAtheVLOGGER]

does anyone know how to generate ca_force.npy ? I have performed md simulations and have .dcd, .vel, .prmtop files.