Thank you!

I am using the parmed.openmm.NetCDFReporter to write NetCDF files (.nc extension), but they cannot be opened in VMD, and MDAnalysis also produces the following error: TypeError: NCDF trajectory .... does not conform to AMBER specifications, as detailed in https://ambermd.org/netcdf/nctraj.xhtml (Net...

Thank you very much! This worked, I combined the atoms in the modeler before creating the simulation.
Alexej

Also tried just now to set positions before first setting positions (so I guess that means before context is created?).
That also does not assign the proper positions to the added particles.
Alexej

Indeed, that could be the reason, but it was not clear to me how I can add particles without having a system.

Currently I am using system.addParticle, and later I was planning to add a nonbonding force only.

How would you suggest to add the particles before system?

Thank you

I am trying to do setPositions for additional particles added, but they are not updated, see code below (using OpenMM 7.7). What could be the problem? Thank you! Alexej from openff.toolkit.topology import Molecule from openmmforcefields.generators import GAFFTemplateGenerator from openmm import * fr...

Can you recommend good tutorials or sample codes for implementing thermodynamic integration with OpenMM?
Thank you
Alexej

The alchemical tutorial https://openmm.org/tutorials works fine in OpenMM 7.7, but inn OpenMM 8.0 produces the error below. Is there an easy fix, or is it better to keep using OpenMM 7.7 for now? --------------------------------------------------------------------------- OpenMMException Traceback (m...

Thank you. In terms of efficiency, it seems that it will be best to first run a full simulation without the particle (or with the nonbonding interactions turned off), and then loop through the trajectory, and recompute the change in energy for a subset of time steps and random positions of the test ...

Super! Thank you so much! I will try this.