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Hi,
I wanted to make sure that I understand the definition of the bias potential matrix correctly.
Assuming an umbrella sampling experiment with 4 windows A, B, C, D and 3 states 0, 1, 2. The restr…
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Dear Lukas
I am trying to use PyDHAMed to compute a PMF for a small molecule crossing a membrane bilayer. I performed umbrella sampling in 1.5Å windows, spanning approx. 7nm (57 umbrellas in total)…
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In the official documentation, only support for the NVT ensemble is found (MD simulation, NVT=true), but nothing is mentioned for the NPT ensemble. How can I implement the MD simulation in NPT ensembl…
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# New term label (required)
MHz X-ray microscopy
# Definition (required)
MHz X-ray microscopy was developed by Dr. Patrik Vagovic and team at the European XFEL (P. Vagovic, Optica 2019.). MHz…
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Add Jupyter Notebook examples on US simulations of particle in a model potential (in OpenMM), for:
- [x] 1D US
- [x] 1D to phi-ensemble reweighting
- [x] 1D to 2D reweighting
- [ ] 2D US
- [ ] …
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I noticed there is a parameter to resample to angular resolution: https://github.com/thi-ng/umbrella/blob/develop/packages/geom-api/src/sample.ts
However, I am not getting the expected result when …
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Trying to run TUU simulation using GPU nodes on stampede:
I. 32 replicas, 1 core per replica, allocate 1 node (16 cores), failed
II. 32 replicas, 1 core per replica, allocate 2 nodes (32 cores), fini…
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Hi OPS developers. These days I'm trying to reproduce the result published in [here](https://pubs.acs.org/doi/10.1021/acs.jpclett.1c03837). In this article, the author computes the relative rate const…
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Hi,
I was running the example scripts for HOOMD-Blue umbrella sampling and I am getting the following error.
******ubuntu-20.04.4.sif I have no name!@cs001 HOOMD]$ mpiexec --mca btl self -np 12…
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Hi !
I am a newbie, I am trying to find some tools to do QM/MM or QM/MM MD with protein and Small molecules.
I think maybe i can use ORCA&Chemshell&some MD software.
But today i find your ASH.
C…