Hi Peter:

It looks like something is wrong with the OpenMM installed on our computer. I wrote a Python script using CustomCentroidBondForce and apparently it works well on another machine. Thank you very much for your help!

No problem! Thank you very much! This code actually sits in the OpenMM-Tinker interface file. So it is pretty bulky. But the only lines I added to this file are: static OpenMM_IntArray* getGroup(int* kgrp, int* igrp, int idx){ int start = igrp[2 * idx] - 1; int end = igrp[2 * idx + 1] - 1; OpenMM_In...

Hi Peter: Thank you for the quick response! I hard-coded the energy expression because I wanted to compare the potential energy at step 0 with and without the CustomCentroidBondForce. Anyway, I just recompiled my code using the energy expression "100000*distance(g1,g2)^2". I compared the potential e...

Hi Friends: Good afternoon! I added a CustomCentroidBondForce between two groups of atoms and apparently it had no effect during the simulation. The two groups of atoms deviated very far away from each other after 500000 steps. I then hard-coded the energy expression to be "10000", added the CustomC...

Hi Peter:

Yes, now I can use "dt" for global computations! Thank you so much!

Hi Jason: Sorry for the confusion! No, I did not define my own "dt". Before Peter posted the fix, I was not able to update one variable "temp" that I defined when using "CUDA" as my platform. Everything works when I use the reference platform. Now with the fix, I can update "temp", but not another u...

Thanks a lot for the quick fix! I re-compiled the code and found out that although the variable "temp" now gets updated correctly, another user-defined variable "c" now doesn't. Although I added the step "addComputeGlobal("c", "exp(-dt/tautemp)")", "c" keeps its default value throughout the entire s...

No problem! Please see attached for the code. Thank you very much for taking the time to help us!! Also, what I have right now is a Verlet integrator. But eventually we'd like to implement a multiple time step integrator. I know I can access a Force object and change its group by forceIndex = 3 forc...

Thanks a lot! I wrote the code for a CustomIntegrator and found out it works correctly on the "Reference" platform but not on "CUDA". The problem is that after I update one variable, for example, the kinetic energy, and want to update the temperature using the kinetic energy I just calculated, the c...

Thank you! One last question: Based on what I read from the documentation, I can access individual forces f0, f1, f2,... etc from within CustomIntegrator. But I can't find what these forces are (harmonic bond forces? Coulomb interaction? van der Waals interaction?). Is there documentation somewhere ...