Alireza Moradzadeh

I see! Please let me know when you upload the example. I am going to use it in coarse-graining applications in a similar fashion as this [repository ](https://github.com/torchmd/mdgrad). They also...

I will take a look thanks!

I mean the Drude force field. Should I change anything particular in the integrator and other details for the Drude force field?

Do you have an example of the SWM4 with ions? I am new to open-mm and would appreciate if I get pdb, psf, py, and xml files for it?

I was wondering if the sigma and epsilon are normal for water based on charm_polar_2013.xml: ``` forces = { force.__class__.__name__ : force for force in system.getForces() } nbforce = forces['NonbondedForce']...

Okay, can I access those parameters? More importantly, since it is running fine, can I be sure it is correct?

Thanks @peastman for the help. I have one more question, I want to simulate fix carbon nanotube but I am not sure which type or residue should I select. Can...

Because what I am looking to do is to freeze CNT, I don't need bonds, angle, and dihedral. What I need is adding a new particle type with only sigma...

Thanks, I found sigma and epsilon. Now, I am trying to figure out how to add them to the charm_polar_2013.xml

The motivation for my work is this for each frame of trajectory, I need to compute neighbor list. This neighborlist should be converted to an edge_index = torch.tensor of shape...