[AMBER] live dCAT simulation

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Thu, 5 May 2016 16:52:40 -0700

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

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 :-)



-- 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 Thu May 05 2016 - 17:00:03 PDT
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