I see. But doing that wouldn't result in any of the "recognized" flexible models without changing charge parameters, etc. in the SPC/E or TIP?P model. Simply letting go of the rigidity seems like a quick-and-dirty way to get flexible water, but I anticipate problems justifying the model...What do yo...

Hi!
Does OpenMM have (or plan to have) an implementation of a flexible water model like SPC/Fw that is compatible with AMBER, etc. force fields for biomolecules? I am considering doing some flexible water MD but I'm not sure I want to switch to something as expensive as AMOEBA right away.
Thank you!

Hi! I need to write out a set of atom positions to a dcd file. These positions won't have topology info - it's just a set of coordinates with size (nAtoms, 3). Is there a way to write a dcd file using just this position data? If I could do that, I could then build a topology matching those positions...

Got it. Thank you!

Actually, I have one followup question. Say I wanted to penalize the molecule moving out of a "vertical tube" with walls defined by force = CustomExternalForce("(step(x-x0) + step(-x0-x))*(k/2)*(x-x0)^2 + (step(y-y0) + step(-y0-y))*(k/2)*(y-y0)^2") force.addGlobalParameter("k", 10 * kilocalories_per...

Thank you for always answering so quickly. I will try the constraints first.

Good morning OpenMM forum! I want to keep a DNA molecule pointed roughly along the z-axis throughout a long simulation. So far I've tried 1) restraining all DNA atoms with a very stiff spring constant and 2) introducing an energetic penalty to the DNA tilting and having x- and/or y- coordinates sign...

Hi! I am trying to set up a temperature replica exchange simulation with openmmtools. The openmmtools documentation doesn't have much detail on the format of the netCDF output of the ParallelTemperingSampler class run method. How can I feed a trajectory reporter into ParallelTemperingSampler to get ...

Hi! I want to do some metadynamics where the collective variable is the distance between two specific particles. I am not sure how to implement the collective variable. Below is the code I have now, which I adapted from https://github.com/openmm/openmm/issues/2126. I am particularly unsure about wha...

good morning, I found a github feature request discussion from 2018 where peastman and jchodera discuss incorporating GROMOS into OpenMM. Did that ever happen? What would be the easiest way to use GROMOS(96) with OpenMM? - thanks, dan

https://github.com/openmm/openmm/issues/1999