# Notebook on particle simulations

**URL:** <https://discourse.julialang.org/t/notebook-on-particle-simulations/68496>\
**Category:** Modelling & Simulations\
**Tags:** notebooks\
**Created:** [September 21, 2021, 12:03am UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496 "2021-09-21T00:03:44Z")\
**Posts on this page:** 8\
**Page:** 2

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**Author:** ![lmiq](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lmiq/32/18314_2.png) [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Post date:** [September 22, 2021, 4:18pm UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/21 "2021-09-22T16:18:40Z")

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I think that if you are willing to try any of the packages we developed, or any other package, the developers will be happy to help. Just let us know 🙂 .

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**Author:** ![liuyxpp](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/liuyxpp/32/9870_2.png) [@liuyxpp](https://discourse.julialang.org/u/liuyxpp)\
**Post date:** [September 23, 2021, 2:09am UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/22 "2021-09-23T02:09:52Z")

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I also can not infer any conclusive results from those benchmarks. It seems VV is indeed the most practical choice in most cases.

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**Author:** ![j\_u](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/j_u/32/219081_2.png) [@j\_u](https://discourse.julialang.org/u/j_u)\
**Post date:** [September 23, 2021, 11:18am UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/23 "2021-09-23T11:18:38Z")

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Thank you @lmiq. I will take it into a consideration.

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**Author:** ![Pongskorn\_Saipetch](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/pongskorn_saipetch/32/15208_2.png) [@Pongskorn\_Saipetch](https://discourse.julialang.org/u/Pongskorn_Saipetch)\
**Post date:** [September 25, 2021, 4:21am UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/24 "2021-09-25T04:21:15Z")

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A small typo: “…Progapating uncertainties in more general scenarios requires the definition of other propagation rules…”

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**Author:** ![Vasily\_Pisarev](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/vasily_pisarev/32/7929_2.png) [@Vasily\_Pisarev](https://discourse.julialang.org/u/Vasily_Pisarev)\
**Post date:** [September 25, 2021, 3:23pm UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/25 "2021-09-25T15:23:19Z")

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Thank you for the reference on pseudo-Verlet list.  
I’ll need to investigate how different strategies of distance check reduction fare against each other.

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**Author:** ![lmiq](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lmiq/32/18314_2.png) [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Post date:** [September 25, 2021, 8:15pm UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/26 "2021-09-25T20:15:27Z")

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> [@Pongskorn\_Saipetch](#):
>
> A small typo

Thanks! fixed now.

> [@Vasily\_Pisarev](#):
>
> I’ll need to investigate how different strategies of distance check reduction fare against each other.

Tested here with different `cutoff/cell size ratios` (the density in the example is about the atomic density of liquid water at room temperature):

With `lcell=1` (i. e. cell side = cutoff):

```julia
NAMD:

real 1m21,954s
user 9m42,817s
sys 0m1,628s

CellListMap:

real 1m33,974s
user 8m26,930s
sys 0m2,114s

```

`lcell=2` (cell side = cutoff/2):

```julia
real 1m15,512s
user 6m25,418s
sys 0m2,531s

```

`lcell=3` (cell side= cutoff/3):

```julia
real 1m46,958s
user 9m24,130s
sys 0m2,930s

```

Thus `lcell=2` seems to be the optimal choice for this system density, which is the typical density of MD simulations. (I will make the default choice automatically set an optimal parameter at some point).

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**Author:** ![Vasily\_Pisarev](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/vasily_pisarev/32/7929_2.png) [@Vasily\_Pisarev](https://discourse.julialang.org/u/Vasily_Pisarev)\
**Post date:** [September 25, 2021, 8:36pm UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/27 "2021-09-25T20:36:06Z")

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> [@lmiq](#):
>
> Thus `lcell=2` seems to be the optimal choice for this system density, which is the typical density of MD simulations.

Yes, but it would depend on the cutoff distance as well. I’d assume you tested with r\_{cut} \approx 2.5\sigma, but one may want to e.g. calculate RDFs up to a much larger cutoff radius. I have a suspicion that a quasi-optimal choice is to strive for a certain average number of particles per cell. There are other things as well, like is it beneficial to build neighbor lists or use cell lists directly. Of course you’d like neighbor lists for MD itself, but they may be worthwhile for post-processing as well if there’s a pipeline with many properties requiring the same cutoff radius.

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**Author:** ![lmiq](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/lmiq/32/18314_2.png) [@lmiq](https://discourse.julialang.org/u/lmiq)\
**Post date:** [September 25, 2021, 8:37pm UTC](https://discourse.julialang.org/t/notebook-on-particle-simulations/68496/28 "2021-09-25T20:37:37Z")

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That test uses cutoff=12 Angs, which Is what I typically use in my simulations.

> [@Vasily\_Pisarev](#):
>
> Of course you’d like neighbor lists for MD itself,

Yes, for actual MD that is important. I have in mind the possibility of something intermediate, which would be tracking the particle displacements and updating the cell lists only for the particles that moved more than the accepted margin. I think that is feasible and maybe be useful for other type of applications than MD (like analysis or optimization, which is where I’m mostly focused).

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