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Reviewer 3 Comment 17:
> The manuscript states that "we need 3200 ethane molecules to achieve low enough uncertainties..." It's unclear why the authors have coupled the uncertainty to the system size…
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Defect Description:
The Simulation page of "Determination of the Molar Absorptivity of a Light Absorbing Molecule" experiment of this lab, improper alignment is observed for the simulation screen. In…
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Hi, I benchmarked a simple system with GAFF and `torchANI` potentials on two different GPUs: GTX Titan X (Maxwell) and RTX 3090 (Ampere). For GAFF, I'm getting a 2x speed on the 3090 compared to Titan…
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I've started investigating whether it's possible to run stable MD simulations using models trained on SPICE. I'm opening this issue as a place to describe my results and discuss approaches.
As a s…
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Hi, I faced some failure during MD simulation with error that one or more water molecules cannot be settled. It could be the system I prepared is somehow incorrect.
After looking into the dual mo…
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When "Calculate Scale Divisor" is used after simulation, the Start values of the molecules appear to be set to NaN.
Use the (internal) example project provided in Mantis, then:
1. Open the simulat…
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I have been looking at the new metadynamics functionality in OpenMM 8.1.1 and I am trying to reproduce a protocol in the following [paper](https://www.nature.com/articles/s41598-022-05875-8#Sec11):
…
mjw99 updated
3 months ago
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### Feature Description:
Here, I propose the introduction of a new feature to enable users to associate tags with each simulation. This feature allows for better organization, search, and analysis of…
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The following parameter nodes are missing in v1.0, but used in the simulation setups:
- volume fraction
- *some molecule* fraction (in particular dendrimer fraction)
@Bondoki which parameters …
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The current approach, wherein we identify molecules in our Topology by using a graph to match reference molecules onto the Topology, results in slightly odd behavior in the case of symmetric molecules…