Closed amin-sagar closed 7 months ago
The short answer, and one I expect will get things working for you now, is here. You can still control bond constraints at runtime in the MDP file.
A more thorough solution would involve allowing the GROMACS writer to write topological bonds that are missing physical interactions. The simple cases seem easy enough but I haven't thought through the trickier cases or written up this behavior. I expect that'll happen in the future but I wouldn't count on it happening immediately.
Thanks @mattwthompson I think I understand the origin of the error. However, if I change
system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME,nonbondedCutoff=1.0*nanometer, constraints=HBonds,hydrogenMass=4*amu)
to
system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME,nonbondedCutoff=1.0*nanometer, constraints=None, hydrogenMass=4*amu)
I still get the same error. Does this need to be done with forcefield_kwargs and can't be done by just changing the constraints to None as I tried?
I understand now. The value of rigidWater also needs to be set to False. So, this works.
system = forcefield.createSystem(modeller.topology, nonbondedMethod=PME,nonbondedCutoff=1.0*nanometer,constraints=None,rigidWater=False)
Thanks for the help. Amin.
Hmm ... I'm glad you were able to get it to work but it'd be great if there was a was to use unconstrained bonds and rigid water since TIP3P and its variants are not flexible water models.
That's true. Can someone with more experience in gromacs suggest a way to make waters rigid after topology generation, by adding some restraints?
Usually people use SETTLE or something like it: https://manual.gromacs.org/current/reference-manual/algorithms/constraint-algorithms.html#settle
Hello. I am trying to save an espaloma parameterized system in gromacs format to run the simulations using gromacs. I posted this issue earlier on espaloma repo https://github.com/choderalab/espaloma/issues/145.
I tried the following script
But I get the following error
I have tried for multiple systems and I always get an error due to missing bond parameters but the simulations run fine. What am I doing wrong? I would be grateful for any suggestions. Amin.