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Thank you very much for sharing the code. I am training a set of ReaxFF parameters against the equation of state of Si3N4 crystal using JAX-ReaxFF. However, I noticed that the error reported by JAX-Re…
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[2wpa.pdb.txt](https://github.com/openmm/openmm/files/13319836/2wpa.pdb.txt)
The following energy minimization ends at a state with max. absolute force element = 7.6e7 kJ/mol/nm.
When I use my o…
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Compositions where one component has a fraction of identical zero are problematic in some methods. Apparently, the minimization works well (which I actually find surprising). However, calculating chem…
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I've noticed the following weird behaviors with `pdbfixer` upon mutating to a Tyrosine. The first one is on the latest stable release, the other is on the latest dev build:
**First issue:**
If I…
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Hi
Thanks for IL topologies. I was just trying to simulate a system bmimpf6. The problem is that if I do energy minimization, it is giving negative potential energy. this is the minimizatio…
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Hi There,
I first want to say that for my cases PDBFixer is superior to other methods. For the case of 7zaw.pdb - Human GPC3 having missing atoms and residues (many) - PDBFixer is able to add the m…
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I had a long discussion with @JNmpi this week, and we still haven't converged on this topic, but I think it's good to write it down to present the progress so far and also for me to organize my though…
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Under the "Restrictions" heading on the bottom of the minimize command manual entry (https://docs.lammps.org/minimize.html), there is a statement you'd be interested in implementing energy minimizatio…
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Dear all,
I am trying to create a pipeline to automate the binding energy calculation of several variants of a homotetrameric protein in complex with a medium/big-sized ligand (CoA). I haven't deci…
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I run the setup_initial_structures.py. It works for first 2 templates but gives an error for 4W56 initial structure. Final solvated potential energy is concerning, so I think something is wrong with m…