I retreived your job on CHARMM-GUI, from one of the files. I downloaded the tar.gz and in the directory /openmm there is a file README. If you execute this file, the simulation runs fine. You will have to change the platform to CPU, from CUDA, but otherwise, I didn't have a problem. Is there a reaso...

Okay, then that sounds perfect. Thanks again!

Thanks Peter!

I think the custom integrator option is probably the best option here. Although, we want to ignore hydrogen atoms in our implementation, which doesn't sound like it is an option? Also, do we loose the flexibility of using functions like sin(x) and cos(x)?

Hey OpenMM developers, I would like to define a force on my system that creates a gradient. The force should be F = z (x-direction), but if I give CustomExternalForce the energy equation "z*x", it will give me the proper x-direction force, but also a z-direction force, right? Is there any way to mak...

Can you provide more information? It isn't clear from your text why the system is crashing...
Is there an output from Python as to why it failed?

That makes sense! Thanks for the thorough explanation and helping me find the source of the problem. I will remove the CM motion remover and try again!

Ah! The last part of your statement is what I was looking for. We were expecting to see a difference in velocity due to the applied force. But if the simulation is removing the CM motion, it would set it back to zero?

Many thanks! Sorry this took so long for me to get you what you needed.

Hey Peter, Due to size, I will give you a link to the zip file. It is approximately 300 MB uncompressed. https://drive.google.com/file/d/1rkuv-ivTaKHkmIL8IiAgsRkt6bPja6SG/view?usp=sharing When I run the simulation, I run it through the scrip "slurm.sh", which runs on a GPU at a national lab. In that...

Okay. My apologies. The custom forces are loaded from an additional file along with some of the other settings. I will include them below. Almost all of these were obtained through CHARMM-GUI. inputs are given in a separate file: nstep = 500000 # Number of steps to run dt = 0.002 # Time-step (ps) ns...

I also added the print statement to verify the custom forces are applied, and the numbers are correct.