Re: [AMBER] live dCAT simulation

From: Bill Ross <>
Date: Tue, 10 May 2016 19:42:22 -0700

I added updates of temp and energy and time, which latter I hope to see
eventually overflow:

Reload page if no molecule shows.

Still thinking about how to inject live forces.. are people busy working
on grants?


On 5/5/16 4:52 PM, Bill Ross wrote:
> I've put up a web page showing a live simulation of dCAT in Generalized
> Born solvent, using sander and cpptraj, with Alexander Rose's NGL
> package on the browser side. (dDOG was not amused :-)
> It renders at one frame per second, rms fitted by cpptraj to the middle
> base. There is an informal info page telling how to set up the Amber
> side of things, which might be useful for teaching, and I give the code
> for the web server side for people who want to broadcast their own live
> dynamics. Suggestions for improvement are welcome, within my framework
> of hillbilly science. A missing bond on the molecule display is a known
> problem.
> The simulation's main purpose is to provide correlated noise to my slide
> show image selection algorithms for AI purposes, which it does through
> cpptraj base angle measurements. Now I would like to translate user
> clicks in this entirely different domain into taps on the simulated
> molecule (or perhaps decaying forces). So I'll need to check a directory
> for tap files at some intervals (or possibly a socket). Probably when
> restrt is written.
> Can any developers chime in on what I'd do next? An easy thing might be
> to rescale some forces, chosen anonymously based on indexing, but it
> would be nice to be able to formulate residue- and atom-level
> descriptions to direct things more specifically. NMR facilities come to
> mind, but I'm not sure how computationally expensive it would be to
> invoke them, nor have I had anything do with NMR code. Maybe pre-define
> a bunch of restraints, then dynamically tweak their weights, though it's
> be nice in general to enable a reach-out-and-touch-anything interface. I
> don't know if any folk want to take a step in the direction of having
> live interaction with sander, but if so maybe it's worth thinking
> through the interface and the design together, and incorporating the
> code I come up with. (The feature is already in NAMD and LAMMPS.. maybe
> I'll even wind up back on the author list :-)
> Thanks,
> Bill
> -- How it's done
> Sander writes to restrt every second, and a background script runs
> cpptraj to RMS fit on 3 A base atoms every second. The javascript in the
> browser requests coordinates every second, and a Servlet on the web
> server picks up the current coordinate set and sends it to the
> javascript, which gives it to NGL to render (NGL loads a pdb at first,
> to figure out how it will render).
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Received on Tue May 10 2016 - 20:00:03 PDT
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