Hi Kennie,
sounds good. Maybe we should do Dave's brief version for the manual (needed
soon!) and then we can expand it for JCIM later this spring/summer.
I won't have bandwidth until after the ACS meeting in a few weeks.
carlos
On Tue, Mar 23, 2021 at 9:42 AM Merz, Kenneth <merz.chemistry.msu.edu>
wrote:
> Hi,
> I’d be interested in helping out and JCIM would love to see this best
> practices/review. Kennie
>
>
> > On Mar 23, 2021, at 9:38 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > great idea Dave. I'd be happy to help (but not take it on alone).
> > But maybe we actually could do this as a review?
> > carlos
> >
> > On Tue, Mar 23, 2021 at 9:34 AM David A Case <david.case.rutgers.edu>
> wrote:
> >
> >> Hi everyone:
> >>
> >> Carlos's post (below) prompted me to think of the following:
> >>
> >> Could we create (for the Amber 2021 Reference Manual), a short,
> annotated
> >> bibliography of selected results for "modern" TI calculations in Amber?
> >> I'm thinking of a list of recent papers, with 1 or 2 sentences about
> what
> >> sorts of problems were addressed. We don't want to draw conclusions
> here
> >> about "accuracy", just make it easier for users (including me!) to find
> >> articles that show how Amber developers (or others) are applying the
> tools
> >> we offer. This would not be a review, just an entry-path into the
> >> literature.
> >>
> >> The obvious problem is that we may have more articles to put in this
> list
> >> than makes good sense, but we can see who volunteers what.
> >>
> >> Other application topics, besides TI, could also benefit from such a
> >> annotated
> >> bibliography.
> >>
> >> Some of this information is already scattered in various places in the
> >> manual, but having such lists (say) as an introduction to various
> chapters,
> >> might be helpful.
> >>
> >> Putting this info on a web page might be another alternative.
> >>
> >> Suggestions (and volunteers) are hereby solicted.
> >>
> >> ...thx..dac
> >>
> >> ----- Forwarded message from Carlos Simmerling <
> >> carlos.simmerling.gmail.com> -----
> >>
> >> Subject: Re: [AMBER] Pmemd to run TI on protein mutations
> >>
> >> we've done calculations on protein-protein binding affinity for sets of
> >> mutations using Amber pmemd TI on GPUs and found (in most cases) very
> good
> >> accuracy vs experiment: ...
> >>
> >> we also have a recent review that discusses accuracy of calculations,
> with
> >> references to recent examples ....
> >>
> >>
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Received on Tue Mar 23 2021 - 07:30:02 PDT
