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The total **concentration of lipid components** (`[lipid]= Nlipid*[water]/Nwater, where [water] = 55.5 M`) doesn't make sense as well as the number of water molecules per lipid for some kind of simula…
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Hi,
I wanted to add both NaCl and KCl to a simulation box by `addSolvent()`, but the method itself seems to only allow adding one type of positive ion at a time. I wonder if there is a clever way t…
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Hi, everyone,
Just as the title says, I'm currently thinking about a problem about the charge screening in vaspsol. If I am doing a calculation about a charged slab with VASPsol, and enabled LAMBDA_D…
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I have read some tutorials and documents. Redefining the forces `setUsesPeriodicBoundaryConditions(True)` may solve this problem.
How to modify my system (with topology and atoms, forces)? I have s…
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I have a use case of BioSimSpace that takes an SDF as input, parameterises the molecule using the GAFF forcefield, writes out just a grotop file. In truth, I do write a PDB file too but I want to only…
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Hi everyone!
We have been experiencing memory leaks when running molecular dynamics simulations with models trained with physics-ml and using the physics-ml openMM interface. I am suspecting that t…
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## Description
When trying to open a Track Particles diagnostic using happi I get the following error:
Error in the ordering of the tracked particles
cannot convert float NaN to integer
```
>…
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I was trying a simulation with two compounds in which one of the compounds is containing boron when i ran the script it is throwing an error like
Traceback (most recent call last):
File "rmg.py",…
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Dear Espaloma developers,
Thanks for this awesome work.
I am running some simulations of protein-peptide complexes where I want to treat protein with Amber and peptide with espaloma as it has some n…
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Dear MACE developers and users,
I've trained a rough model for liquid water (using periodic box). If this model is applied to evaluate the energies of geometries in the training set, the obtained ene…