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In manuscript EC12092, Clementi et al. describe a boundary element method at the electrostatic limit to simplify the numerical calculation/analysis for bio-sensing using nanoplasmonics. Due to the con…
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Hello,
First of all I'd like to thank you for creating the AMOEBA force field files for the POPE lipids. I have been trying to run a pure POPE bilayer system using the scripts available here. I am …
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One thing Peter pointed out when testing was that when specifically looking at the Interactions/byEntity calls was that we should also use the 'type' of interaction it is. Getting information about w…
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## Overview
Although Series 4 is the current _de facto_ series of interest, there seem to be some open questions regarding series 3 (S3). For example, it is still unknown which target is hit by se…
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Dear Khalak,
I found there are many clashes when aligning the decoupled structures of ligands in solvent into the apo state pocket. And some of them cannot be solved by just do a minimization and t…
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Hello,
I am trying to do inference with the trained model with new time points. How do we do that? Can you help?
I tried using global_model.predict however it only gave the same results. Is the…
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Hello,
I am currently trying to assign protonation states of a protein through the estimation of the pKa values. I am wondering about the output of the Coulomb interactions and I would appreciate i…
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If we try to launch the benchmark with an non existent kernel WGSIZE, the program actually gives you an invalid result instead of reporting this and terminating early:
```
miniBUDE:
compile_com…
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### Team Name:
qnyble
### Project Description:
RNAs are nucleotide polymers fundamental to a diversity of elementary biological functions, including the (de)coding and regulation of genes, …
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Although Poisson-Boltzmann is not our priority, we have to start thinking how this implementation should be. Let's use this issue to collect some ideas.
There is a widely used tool to solve the Poi…