[gmx-developers] Kick-off meeting for free energy synchronization

Fri Apr 9 08:01:15 CEST 2021

Hi, all-

I've reorganized discussion into one main meta-umbrella issue:

https://gitlab.com/gromacs/gromacs/-/issues/3945

See the subtopics listed there for further discussion.  I've tried to record the main decisions/suggestions from the meeting, but please update and continue the conversation there. I've tried to articulate the main tasks in each subarea, please expand and clarify!  

If you have a vested interest in a given area, make comments and participate in the discussion so that we will remember to include you in any necessary Zoom calls to follow! 

Best,
~~~~~~~~~~~~~~~~
Michael Shirts
Associate Professor
michael.shirts at colorado.edu
http://www.colorado.edu/lab/shirtsgroup/
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

On 4/6/21, 11:42 PM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael R Shirts" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael.Shirts at Colorado.EDU> wrote:

    Reminder of meeting to discuss plans for free energy functionality Wednesday, April 7th, before the next GROMACS biweekly meeting, 9 pm Beijing / 3:00 pm Stockholm / 7:00 am US Mountain  / 9:00 am US Eastern , for max 90 min (hopefully less?), so there is a break before the main GROMACS dev meeting.  

    We can use this Zoom call: https://cuboulder.zoom.us/j/96788997668 (unless people in Stockholm would prefer to use one there - just email that out if you'd like to change it.

    Also, a reminder of the document with loose agenda and people's wishlists here: https://docs.google.com/document/d/15IHzKqe_Ca_d6B2UZtyZz7VcjHag9uYw2uvCe-WKYiI/edit?usp=sharing

    Best,
    ~~~~~~~~~~~~~~~~
    Michael Shirts
    Associate Professor
    michael.shirts at colorado.edu
    http://www.colorado.edu/lab/shirtsgroup/
    Phone: (303) 735-7860
    Office: JSCBB C123
    Department of Chemical and Biological Engineering
    University of Colorado Boulder

    On 3/28/21, 11:16 PM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael R Shirts" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael.Shirts at Colorado.EDU> wrote:

        Hi, all-

        Based on the response, it seems that Wednesday, April 7th, before the next GROMACS meeting. I propose 3:00 pm Stockholm / 7:00 am US Mountain  / 9:00 am US Eastern, for max 90 min (hopefully less?), so there is a break before the main GROMACS dev meeting.  

        I have started an initial document here:  https://docs.google.com/document/d/15IHzKqe_Ca_d6B2UZtyZz7VcjHag9uYw2uvCe-WKYiI/edit?usp=sharing

        I've tried to lay out some of the main software questions that have come up - please add comments and edits. 

        Perhaps more important is a section at the end where people can put what THEY want to see happen in GROMACS with respect to free energy calculations/functionality, including what you are working on now. Please add your name and your wishlist in this section here!  If you are advocating for inclusion of a method, please provide a link to reference for the method. Bullet points are fine.

        I propose everyone try to put down what they want to see by end of day Wednesday, March 31st. I will attempt to do some organization after that and put together an agenda for the 7th.  Hopefully after that point, there will be enough organization to start making an set of issues in GitLab (some of which may simply to be decide things to be coded, not code things themselves).  

        I have no illusions we will reach any real decisions by the end of one meeting, but we should have a good sense of what people are working on, what they want to be in GROMACS, and have a good list of the decisions that will need to be made.

        Best,
        ~~~~~~~~~~~~~~~~
        Michael Shirts
        Associate Professor
        michael.shirts at colorado.edu
        http://www.colorado.edu/lab/shirtsgroup/
        Phone: (303) 735-7860
        Office: JSCBB C123
        Department of Chemical and Biological Engineering
        University of Colorado Boulder

        On 3/26/21, 12:36 PM, "gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael R Shirts" <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se on behalf of Michael.Shirts at Colorado.EDU> wrote:

            Hi, all-

            Please indicate times you are available for the discussed free energy synchronization meeting (here: http://whenisgood.net/gmxfreeenergystart if you are developing free energy-related methods for GROMACS!)  I've focused on Wed morning US/ late afternoon Stockholm for the next 3 Wednesdays (except for the time of the bi-weekly GROMACS meeting itself). 

            I will send out an agenda with notes, proposed outcomes for the meeting, and a little bit of homework for people by Monday morning (US time) for people to look over and comment on before the meeting.

            Please pass this on to people I didn't include that may not be on the gmx-developers mailing list. 

            Best,
            ~~~~~~~~~~~~~~~~
            Michael Shirts
            Associate Professor
            michael.shirts at colorado.edu
            http://www.colorado.edu/lab/shirtsgroup/
            Phone: (303) 735-7860
            Office: JSCBB C123
            Department of Chemical and Biological Engineering
            University of Colorado Boulder

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