That's great! Please let me know if you have any more issues.

Hello Manuel, Thanks for posting your question. When the liquid bromine example runs, it actually executes a script "rungmx.sh" which then executes a Python script "npt.py". It is important that "rungmx.sh" sets the environment variables correctly so that "npt.py" can import the ForceBalance modules...

Ah, thanks for coming back with the update. I admit I didn't see your earlier message.

If your changes to the code are useful in a broader context, would you consider contributing it back to the main repository at github.com/leeping/forcebalance ?

Thanks,

- Lee-Ping

Thanks a lot. That seems a lot simpler than creating a fictitious atom.

Hi there, If I wanted to restrain the center of mass of a molecule to a particular position (without restraining the individual atoms), should I use the CustomCentroidBondForce? I could create a fictitious particle with no mass and no other interactions so that it stays at a prescribed position, and...

Glad to hear it. Yes, please stay in touch.

- Lee-Ping

Ahh, I think I know what's going on. Thanks for the error report. With the current AMBER version, I don't think it correctly loops over the whole trajectory when writing the forces; instead it just writes the first force and quits. Additionally, it prints out the force components (i.e. bond, angle e...

Hi Isaiah, Thanks for your message. I'm glad you're interested in using ForceBalance. ForceBalance does support AMBER for parameterizing force fields, but it can't convert a GROMACS force field format to AMBER. If you change AbInitio_GMX to AbInitio_AMBER, you also need to change some files in force...

Hi Sean, I know about this problem, and it comes from a recent (<6 mos.) change to the OpenMM API. You're probably linking against version of OpenMM that is too old, and it doesn't have the API change. Try with the newest development build of OpenMM (git clone https://github.com/pandegroup/openmm) a...

Hi Peter, I don't know all the nuts and bolts of how common batch systems work (e.g. PBS, SGE, Slurm), but my impression is that they do not place actual restrictions on the number of cores when a user submits a job. It's up to the user to restrict the number of cores that are used. This is distinct...