Tinker is a molecular modeling and computations package geared towards high-speed calculations on large systems and molecules. It comes with a java-based interface called "Force Field Explorer", which is still under development - i.e. it is sometimes quite cranky and unstable, depending on the version of JRE and Java3D you have installed. Tinker itself, however, which runs from the command line, is rock-solid. Reproducible: Always Steps to Reproduce: 1. 2. 3. This package depends upon Java3D for FFE, and FFE is totally unstable with the 1.3.1 beta of Java3D. As a result, you should use the 1.3-FCS version with this package for right now. Though FFE is problematic, the core Tinker application, as stated above, works very well, and is very stable. Tinker is VERY fast when it comes to large-scale computations.
Created attachment 22301 [details] Tinker 4.1 ebuild
Ah, cool. This is one of the things I've wanted to get to but haven't had the chance. I'll look at it soon.
Created attachment 26329 [details] Updated Tinker 4.1 ebuild This is a full ebuild for Tinker 4.1 which fixes the problem associated with the missing parameter files. Energy minimizations now work fine - all parameter files are now properly placed into the "/usr/local/tinker/params" directory where the belong.
Gentoo can't install to /usr/local, that's for personal use. We stick to /usr.
Created attachment 26330 [details, diff] DIFF patch to fix the paths for the ebuild This patch fixes all of the destinations to the proper /usr/tinker directory.
Created attachment 26333 [details, diff] Diff to fix Tinker ebuild to use the Java3D now in Portage Now depends upon dev-java/blackdown-java3d.
I think the version of Java3d in Portage works ok now. With the path fixes and the portage Java3D, the Force Field Explorer GUI runs pretty well, being much less prone to random crashes. I think all things being equal, this is about as stable as this package is going to be short of actual updates on the part of the program itself. I'll make an updated ebuild for this app to use ICC/IFC during compilation, and upload a full ebuild. Other than that, though, I think this one is about as good as it's gonna get.
For the ICC/IFC stuff, make sure it doesn't use USE flags. It should just respect the environment variables $CC and $FC.
Please turn all the spaces indenting the various parts into tabs. I'd like to take a look at this.
WebMO 5.0, just released, added support for >=tinker-4.2. Since I'm a huge fan of WebMO, I've suddenly become more interested in making something happen with this. I emailed the upstream author and requested a friendlier distribution style, with a versioned tarball.
By the way, 4.2's distribution method really sucks, the way it looks. There's crap all over the place, and most of it isn't even in the (unversioned) tarball.
That's an understatement. I did spend some time messing with it, but was unable to figure out how to manually dig out all of the necessary files out of the distribution - I was able to update the tinker executables themselves to the 4.2 rev, but the ffe GUI is still a nightmare. Since I have no experience with JBuilder or building java apps period, I'm not sure how to proceed on this. In theory, I would suggest we go with grabbing the tinker source executable from: ftp://dasher.wustl.edu/pub/tinker.tar.gz And the FFE source from: http://dasher.wustl.edu/ffe/ffe-source.jar And compiling ffe from the source. It's really a shame that the distribution method is so bad - as I'm forced to use the Windows version now. Sadly, the 4.2 rev, when installed, works VERY well. I still use it via CLI on a linux box to do long-term calculations, but for simple stuff I use the Windows one, since that is the only thing which plays nice for the time being.
I just got an email from Jay Ponder that basically said, (summary) "We won't make it easier to start using because it's difficult to use properly once it does work." We'd probably be better off just creating a custom tarball with whatever we need in it, in addition to the tinker.tar.gz.
I've just added tinker-4.2 to the tree, but I can't get FFE working. I'd really appreciate if you could take a look at that.
