Jmol: 3D visualization of F@H projects

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Jmol: 3D visualization of F@H projects

Postby NicoV » Thu Jan 19, 2012 8:32 pm

(Topic recreated from old forum)

To see F@H projects in 3D: http://www.jmol.org/fah/?view=b (the view=b parameter is for viewing also beta WU).

If you have files for some missing projects, please send them to me by mail (nvervelle at gmail dot com or nico at jmol dot org or nicove at users dot sourceforge dot net) : I am looking for the file named current.xyz in the work folder.

For Amber projects, I can also use the topology and trajectory files produced by the Amber core. Compared to .xyz files, they contain a lot more information and especially several frames that can be played in a animation. I am looking for the files named wudata_xx.top and wudata_xx.trj when the completed percentage of the wu is near 100% (the best is 98% or 99%) to have the maximum number of frames in the files.
This feature is currently under development, but I am already looking for the files.

Some projects (e.g.- the GPU core) do not produce a file called current.xyz. There's not much we can do about it.

You can send the .xyz file as soon as the processing has started on your computer. The current.xyz files already contains atom coordinates (the coordinates are just updated when the calculation is running).

If you are interested in writing a tool for automatically sending the files, you may use the following files for knowing what files I already have or what files I am looking for:
- The list of current.xyz files I already have is kept updated at http://www.jmol.org/fah/availableProjects.txt
- The list of current.xyz I am looking for is kept updated at http://www.jmol.org/fah/missingProjects.txt
- The list of topology+trajectory files (Amber) I already have is kept updated at http://www.jmol.org/fah/availableAmber.txt
- The list of topology+trajectory files (Amber) I am looking for is kept updated at http://www.jmol.org/fah/missingAmber.txt

I have written a small Java tool for this (see here).

It's a Java program, so you need Java on your computer.
To use it, unzip the files, double-click on JmolFah.jar (or execute java -jar JmolFah.jar), configure the tool (mail, username, ..., directories) and let it check for interesting files.
If you want, you can create a scheduled task (or equivalent, depending on your OS) to run it on a regular basis (every hour, every day, ... up to you)
NicoV
 
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