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1. The gamma in the Brownian dynamics is not clearly defined, there should be equations specifying the gamma is 6pi eta R/m, not 6 pi eta R
2. The Mass property in the brownianState object is not use…
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I did a quick exploration of the Vivarium Web site, which was pointed out to me by Matthew Akamatsu at a workshop on synthesis of scientific knowledge (in which @eagmon also participates). Here's some…
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Rough idea, might be not precise:
- Once there was no life. There was just inanimate matter, molecules flying everywhere.
- Organic matter formed into nucleic acids
- The first organic compounds …
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Hi. Fellow physics+audio nerd.
I'd love to see a smooth-random LFO module based on simple Brownian motion. Basically, add a random nudge at regular (or exponentially distributed intervals) with, sa…
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@vavachan, lets shift focus on diffusion near a wall, just for a while. What we want is that the particle maintains a roughly steady z-distance from the wall, but is free to move in the x-y plane othe…
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When they are not happy if there is a single of the other shape near them (I.e.: They are extremely shapeist), segregation slowly goes down over time.
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**Describe the bug**
I've recently been trying to implement multiple distance restraints for absolute binding free energy calculations in BioSimSpace and SOMD ([modified BSS](https://github.com/fjcla…
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Dear Dr. Ondrej Maxiam,
I am using “SlenderBody” source code to do my simulations. I am modelling the hydrodynamic interaction of sedimentation of a pair of fibres with consideration of Brownian mo…
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I've had a quick shot at running ABFEs with SOMD2. The overall experience was a massive step up from SOMD! The recent sire documentation was also super clear and comprehensive. However, I've had a cou…
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- [ ] how to set rng seed
- [ ] how to override a constant value (e.g., gravitational accel.)
- [ ] how to enable dimensional analysis (so that si.* are not unitless)
- [ ] how to define a new coll…