I added some of our recent work using Amber TI to this google doc, feel
free to add yours and then we can put everything in the manual (or Dave if
you want us to merge them individually that's ok too).
Dave let me know if you think these descriptions are too long.
carlos
https://docs.google.com/document/d/1WPqg8U6Y-tR9YZKXwO0kTZJ9fPmuy5kuKO2Nq2-Xsb0/
On Tue, Mar 23, 2021 at 10:01 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 Wed Mar 24 2021 - 11:00:02 PDT
