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I am trying to set up some MD runs to simulate a series of small molecules against a reference protein target using AMOEBA, and was able to generate parameter files for the small molecules in poltype2…
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# 216 water
case 1: Total time used: 13.20 hours
case 2: Total time used: 1.41 hours
case orientation: Total time used: .40 hours
```json
{
"name": "216h2o-240ps-mbx-pol.xyz",
"system":…
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I am not very familiar with GCMC simulations, so this is perhaps just ignorance on my part. However, I still haven't been able to figure it out. When I run [examples/gcmc_adsorption.py](https://github…
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- [x] Journal Ideas
- [ ] List of tasks to be completed and to be mentioned in the manuscript:
- [x] working on PiP (#55) and all platforms (#27 ):
- [x] working damping (#48) and parameters for …
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Hi.
I'm trying to simulation alkali halide clusters in gas phase.
I want to maintain its structure during the simulation, and it must move, rotate during the simulation.
Therefore, I can't us…
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Dear Sir,
I have completed running trajectories in the SHARC-LVC interface and then diagnosed each trajectory using the $SHARC/diagnostics.py script. The problem I am encountering is that I get diffe…
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I am trying to learn to use this software for the purpose of simulating a microtubule dataset of fluorescence fluctuations for reconstruction, but I have just started to get in touch with simulated da…
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A few step in the current workflow will become rate-limiting at large scales:
- [ ] Inferring hydrogen positions for linkers
- [ ] Linker filtering (checking if they are single molecules, etc) tak…
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Either missing or I was not able to find it. Yes, there is at least the `ppafm/examples/pyridineDensOverlap` example and `ppafm/examples/paper_figure` can be used as another example for the GPU versio…
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A simulation frame is represented by a `FrameData` that is sent as a single gRPC message. Because a gRPC message is limited by default to 4MB, a frame is limited to what can be represented in that vol…