Cool. It shouldn't be too hard to use it as an MD backend for IMP (with supported for whatever restraints can be easily mapped onto their standard terms).

On Sep 24, 2009, at 4:05 PM, Andrej Sali wrote:

> John: > > It was good to see you too - you never change - always smiling! > > Thanks for this pointer - I cc-ed the whole lab so everybody can > check it out and see if it is helpful for their project. It does > look as if at least our IMP (and MODELLER) developers should take a > very good look. > > Many thanks again, > > Andrej > > Begin forwarded message: > >> From: John Chodera jchodera@gmail.com >> Date: September 24, 2009 1:27:39 PM PDT >> To: Andrej Sali sali@salilab.org >> Subject: OpenMM >> >> Hi Andrej, >> >> It was good to run into you again today! It's been far too long >> since >> I've been back to visit folks at UCSF, I think! >> >> I wanted to send more information on the OpenMM toolkit that I had >> mentioned earlier. Vijay Pande (among others) at Stanford is helping >> guide the team that is developing it. The project itself is LGPL, >> and >> can be obtained from the SimTK site here: >> >> http://simtk.org/home/openmm >> >> The toolkit contains a simplified API that makes it very easy to plug >> in the molecular mechanics engine, as well as a number of >> implementations of this API for either CPUs or NVIDIA GPUs (with an >> OpenCL implementation coming soon). The current NVIDIA GPU >> implementation is almost embarrassingly fast: Using a modern GB/SA >> solvent model with no cutoffs, you can crank out simulations 500 - >> 1000 times faster than on single CPU cores. They've also recently put >> in explicit solvent simulation capability with PME, though it's not >> quite as fast. The size of the system you can simulate is limited >> only by the amount of graphics card memory you have, but even >> standard >> gaming cards like the NVIDIA GeForce GTX 285 have 1 GB and can fit >> probably thousands of residues. >> >> The toolkit is in C++, but there is also a set of Python bindings >> (wrapped via SWIG) available here: >> >> https://simtk.org/home/pyopenmm >> >> They're still working toward a 1.0 release, so some of the features >> that will be most useful for reimplementing MODELLER restraints >> aren't >> in yet, but will be in there soon. The drawback is that, to get the >> enormous speedup, all force calculations must be done on the GPU, >> which typically require special coding for special force terms. They >> currently have standard harmonic bond and angle terms, periodic >> torsion terms, Lennard-Jones and Coulomb terms, a couple of GB >> models, >> and a number of integrators and thermostats. What is most exciting >> is >> their 'CustomNonbondedForce', where you simply specify a *string* >> that >> is a Mathematica-like algebraic expression for your interatomic >> energy >> term, as well as algebraic expressions for parameter mixing rules, >> and >> it will automatically differentiate it and figure out how to compute >> the forces on the GPU for you! A similar 'CustomBondedForce' will be >> added soon that will allow easy implementation of all kinds of >> MODELLER restraints. >> >> I've used OpenMM recently to implement a new code for running free >> energy calculations [http://simtk.org/home/yank], and I've been very >> impressed with how well it works. Feel free to pass my contact info >> on to anyone who ends up playing with it in your lab and might have >> questions. >> >> All the best, >> >> John >> >> -- >> John D. Chodera >> QB3-Berkeley Fellow, University of California, Berkeley >> email: jchodera@gmail.com >> mobile: 415.867.7384 >> url: http://www.choderalab.org > <friedrichs-openmm.pdf> > -- > Andrej Sali, Ph.D. > Professor, Department of Bioengineering and Therapeutic Sciences > Director, California Institute for Quantitative Biosciences at UCSF > Department of Pharmaceutical Chemistry > University of California at San Francisco > UCSF MC 2552 > Byers Hall Room 503B > 1700 4th Street > San Francisco, CA 94158-2330, USA > Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 > Assistant, Ms. Hilary Mahon, Tel +1 (415)514-4228; Lab +1 (415) > 514-4233, 4258 > Email sali@salilab.org; Web http://salilab.org > > > > > > >