Search found 20 matches

by Ross Gunderson
Fri Aug 09, 2019 2:21 pm
Forum: OpenMM
Topic: Error from atom_type in PSF file - from CHARMM-GUI
Replies: 4
Views: 92

Re: Error from atom_type in PSF file - from CHARMM-GUI

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...
by Ross Gunderson
Thu Aug 01, 2019 1:04 pm
Forum: OpenMM
Topic: Creating a non-conservative force
Replies: 4
Views: 63

Re: Creating a non-conservative force

Okay, then that sounds perfect. Thanks again!
by Ross Gunderson
Thu Aug 01, 2019 12:48 pm
Forum: OpenMM
Topic: Creating a non-conservative force
Replies: 4
Views: 63

Re: Creating a non-conservative force

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)?
by Ross Gunderson
Thu Aug 01, 2019 11:28 am
Forum: OpenMM
Topic: Creating a non-conservative force
Replies: 4
Views: 63

Creating a non-conservative force

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...
by Ross Gunderson
Tue May 28, 2019 12:11 pm
Forum: OpenMM
Topic: OpenMM (MD) calculations crash during equilibration step
Replies: 1
Views: 135

Re: OpenMM (MD) calculations crash during equilibration step

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?
by Ross Gunderson
Fri Apr 19, 2019 12:16 pm
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 357

Re: External force applied but not effective

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!
by Ross Gunderson
Fri Apr 19, 2019 6:42 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 357

Re: External force applied but not effective

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.
by Ross Gunderson
Wed Apr 17, 2019 7:34 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 357

Re: External force applied but not effective

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...
by Ross Gunderson
Tue Apr 16, 2019 11:04 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 357

Re: External force applied but not effective

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...
by Ross Gunderson
Tue Apr 16, 2019 7:45 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 357

Re: External force applied but not effective

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