I hear you - and GO could have a place. But, at Vanderbilt, we are seeing
10E23 speedups in MD using quantum computing algorithms running inside our
NMR tubes.
This approach is that it solves the sampling problem - and we know all
possible protein/ligand conformations and bound/intermediate states, etc in
these simulations.
Unfortunately, there is no way yet to transfer the outputs back to our
legacy systems for cpptraj analysis - and we find ourselves staring
wistfully at the tubes, only able to report in the literature the relative
clarity of the solvent used. Maybe GO will be the bridge we have been
looking for. Thanks for the report.
https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_quantum_computer
On Fri, Apr 1, 2016 at 7:48 AM, Thomas Pochapsky <pochapsk.brandeis.edu>
wrote:
> Fair enough, Adrian,
>
> But how do you explain David Case? I met his physical instantiation in
> the 1980s, long before the technology was sufficiently advanced for
> downloading AI into a biological matrix.
>
> Tom
>
>
> On 4/1/16 7:31 AM, Adrian Roitberg wrote:
> > On behalf of the Amber developers, I want to come clean about a set of
> > experiments gone wrong.
> >
> > We never thought it would go this far, but it is obvious we must stop
> this.
> >
> > Dr. Jason Swails is in fact a bot, that started form some early coding
> > Chris Schafmeister did as a graduate student, written in CLasp. You can
> > trace this program all the way to the current Google/AI incarnations.
> >
> > That Jason Swails is not purely human should have been obvious to
> > everyone. Do you really believed a single human could have written
> > Parmed AND answer every email to the amber list within 2 minutes. His
> > name is in fact an anagram, check it out.
> >
> > Anyways, the story continues when a research group in southern NY state
> > learned how to incorporate the AI into stem cells, creating a red-headed
> > embodiment of the program.
> >
> > As it turns out, the program was so good that it in fact has added
> > gravity to Amber and its force fields, and indeed, Gomacs is amazing
> > (yes, there is app for that).
> >
> > Please contact Dr. Swails directly, he will respond immediately.
> >
> > Adrian
> >
> >
> > On 4/1/16 6:32 AM, Jason Swails wrote:
> >> Hi everyone,
> >>
> >> I'm excited to announce the next generation of molecular dynamics
> software
> >> suites, which is the result of a complete rewrite of all core routines.
> >> The impetus behind this effort is Google's new, highly concurrent
> >> programming language called Go. Sporting lightweight coroutines
> >> (affectionately called goroutines in the language) with resizeable
> stacks
> >> starting at ~2 KB, there is virtually no limit to the parallelism
> attained
> >> with this new technology.
> >>
> >> Unlike traditional threading models--like POSIX threads (pthreads) and
> >> OpenMP--goroutines take up little space in memory, meaning that this
> >> rewrite will be necessary to take advantage of the new CPU architecture
> >> coming from chip manufacturers that will put hundreds of thousands of
> CPU
> >> cores in a single commodity workstation.
> >>
> >> Originally rolled out for the Apple operating system and hardware, we
> are
> >> calling this new software GoMacs. Gomacs will lead our field into the
> >> future of computational molecular modeling, allowing us to run
> simulations
> >> on the millisecond timescale within just a few days.
> >>
> >> Future plans for Gomacs include a Windows port that will make it
> possible
> >> to study entire viruses at an unprecedented level of detail.
> >>
> >> Wishing you all success in your upcoming research, and an enjoyable
> weekend,
> >> Jason
> >>
>
>
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Received on Fri Apr 01 2016 - 06:30:03 PDT
