Search found 15 matches

by Ross Gunderson
Fri Apr 19, 2019 12:16 pm
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 167

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: 167

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: 167

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: 167

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: 167

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.
by Ross Gunderson
Tue Apr 16, 2019 3:34 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 167

Re: External force applied but not effective

Sure. Below is the file I use to run the simulation. Let me know if theres a detail you think is missing. """ Generated by CHARMM-GUI (http://www.charmm-gui.org) openmm_run.py This program is OpenMM running scripts written in python. Correspondance: jul316@lehigh.edu or wonpil@lehigh.edu Last update...
by Ross Gunderson
Mon Apr 15, 2019 12:11 pm
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 167

Re: External force applied but not effective

Sure! Basically we are trying to apply a solvent flow by applying a constant force to every atom in the solvent. We expect the profile to be similar to a Couette flow model, where the velocity of the flow varies with the height above the stationary plane [which explains why I plot them vs z position...
by Ross Gunderson
Mon Apr 15, 2019 11:03 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 167

Re: External force applied but not effective

Well, I am sure from the graph, the force is applied. When running in equilibrium the two forces are centered on zero.
by Ross Gunderson
Mon Apr 15, 2019 10:31 am
Forum: OpenMM
Topic: External force applied but not effective
Replies: 15
Views: 167

External force applied but not effective

Hey everyone, Sorry to keep posting, but it seems when I respond the forum seems to die. Does anyone have an idea as to why an applied force on a set of atoms would be ineffective to changing the velocity? In my simulation, I am applying a constant force to all water in X, which I can see from the o...
by Ross Gunderson
Tue Apr 02, 2019 8:59 am
Forum: OpenMM
Topic: External force on Solvent
Replies: 4
Views: 118

Re: External force on Solvent

I wanted to follow up on this thread and hopefully it will be noticed. I've attached two plots from my simulation. One plot shows the average forces on each solvent molecule in the x and y directions, plotted in the z-axis. This graph shows the x-direction force with a clearly larger value. Then the...