Lin and I added a couple papers as well. Kennie
> On Mar 24, 2021, at 1:49 PM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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://urldefense.com/v3/__https://docs.google.com/document/d/1WPqg8U6Y-tR9YZKXwO0kTZJ9fPmuy5kuKO2Nq2-Xsb0/__;!!HXCxUKc!hSikSgz5oE4C87PDpiod-nCOX4yWNrQ3jZ48qRedjY0pV9bGr_KV_6Se1TbS7xSjVV6-$
>
>
> 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 Fri Mar 26 2021 - 11:00:02 PDT
