Re: [AMBER] Regarding DiscoverEdges.py script to get xml files for Advanced TI calculation analysis:

From: Kankana Bhattacharjee via AMBER <amber.ambermd.org>
Date: Tue, 10 Sep 2024 20:16:30 +0530

Ok. Thanks a lot.

On Tue, Sep 10, 2024 at 8:12 PM Timothy Giese <giese025.rutgers.edu> wrote:

> The ACES tutorial needs to be updated. It refers to tools that are no
> longer used. You are correct that you should use edgembar rather than
> graphmbar. Once you have the edgembar input xml file, you should run the
> edgembar program. The edgembar output will be written to a file, which
> happens to be a python script. Running that python script without any
> options will create an HTML report containing the free energy and
> convergence information for all trials, stages, and environments. If you
> have multiple edges, then independently run edgembar on each edge. You can
> perform a networkwide analysis and write a HTML graph report using
> edgembar-WriteGraphHtml.py (the edge outputs are the inputs to this
> script). There is online documentation for edgembar here:
> https://rutgerslbsr.gitlab.io/fe-toolkit/edgembar/index.html.
> Specifically, refer to the section labeled "General Workflow" which gives a
> quick overview of the procedure. The documentation also walks through an
> example using some toy data. The data is included with the source code at
> https://gitlab.com/RutgersLBSR/fe-toolkit. One can also directly download
> the data here:
> https://gitlab.com/RutgersLBSR/fe-toolkit/-/blob/master/public/edgembar/data.tar.gz?ref_type=heads
>
>
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Received on Tue Sep 10 2024 - 08:00:02 PDT
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