[gmx-developers] plans for GROMACS 5.0 beta December 1

[Florian Dommert]

> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org [mailto:gmx-developers-
> bounces at gromacs.org] On Behalf Of David van der Spoel
> Sent: Saturday, September 28, 2013 12:05 PM
> To: gmx-developers at gromacs.org
> Subject: Re: [gmx-developers] plans for GROMACS 5.0 beta December 1
> 
> On 2013-09-28 11:10, Florian Dommert wrote:
> > Hi,
> >
> >   just a question regarding update of tools. I sent you quite a time
ago, an
> > improved version of g_pme_error, which is much fast than the current
one, is
> > able to tune the splitting parameter and grid spacing, and is completely
> > based on an analytical calculation. This means that the MC approach to
> > estimate the self-error is not required anymore. The results are
contained
> > in my PhD thesis which is available from:
> >
http://elib.uni-stuttgart.de/opus/volltexte/2013/8179/pdf/Dissertation_Flori
> > an_Dommert.pdf
> >
> > The corresponding part starts on p.50ff
> >
> > The error estimate is working for the SPME and PPPM-AD. The code is
neither
> > present in the master branch nor in the 4.6 branch, but I realized that
> > gmx_pme_error is already slightly converted to C++ code, which means
only
> > the type casting has been changed.
> > Are there any plans to include this new version?
> >
> The only way to get anything in is to port it to the master branch and
> upload it to gerrit.gromacs.org

The only reason why I am asking is, that in June there was already some
correspondence with Mark and Rossen. It sent them the prepared code for 4.6,
but it did not get into the branch. Now I left the university and quite busy
with my work in industry. Actually I was just curious, because it is not my
loss, I just wanted to remind you that there is an updated version and it
would be very nice for Gromacs to have it, because it would be then the only
all-atom MD package, which can do such a tuning.

/Flo
> 
> > /Flo
> >
> >> -----Original Message-----
> >> From: gmx-developers-bounces at gromacs.org [mailto:gmx-developers-
> >> bounces at gromacs.org] On Behalf Of David van der Spoel
> >> Sent: Friday, September 27, 2013 9:13 PM
> >> To: gmx-developers at gromacs.org
> >> Subject: Re: [gmx-developers] plans for GROMACS 5.0 beta December 1
> >>
> >> On 2013-09-27 20:46, Justin Lemkul wrote:
> >>>
> >>>
> >>> On 9/27/13 2:21 PM, David van der Spoel wrote:
> >>>> On 2013-09-27 19:45, Justin Lemkul wrote:
> >>>>>
> >>>>>
> >>>>> On 9/27/13 1:43 PM, David van der Spoel wrote:
> >>>>>> I have a ton of code, most of it won't make it. But here's what
will:
> >>>>>>
> >>>>>> - WAXS/SAXS refinement in mdrun
> >>>>>> - New analysis tool for RNA
> >>>>>>
> >>>>>> Hopefully:
> >>>>>> - QM/MM framework
> >>>>>> - Gaussian output to GAFF topology including RESP (needs OpenBabel
> >>>>>> linking though)
> >>>>>>
> >>>>>> If people want any new polarization stuff, let's discuss it on the
> >>>>>> list. If
> >>>>>> there is interest I can add my coulomb integrals code (Gaussian,
> >>>>>> Slater, need
> >>>>>> CLN and GMP libraries) even though the routines that actually use
it
> >>>>>> will not
> >>>>>> make it before Dec 1st.
> >>>>>>
> >>>>>
> >>>>> I'd be glad to have the conversation about polarization.  I
understand
> >>>>> you may have already had some discussions with Alex about it?
Either
> >>>>> way, if we can pool our efforts (via this list or via direct email),
> >>>>> that would be great.
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>> As far as I understand you were going to implement the Charmm
> >>>> polarization
> >>>> features into gromacs right? I have indeed chatted with Alex a few
> >>>> times about
> >>>> this.
> >>>>
> >>>
> >>> Yes, that is the plan on our end.  I'm trying to keep up with the
mdrun
> >>> cleanup so that whatever I do integrates (no pun intended) with the
new
> >>> framework cleanly.
> >> Good!
> >>
> >>>
> >>>> Tsjerk also mentioned being interested, but I don't know what he's
> >>>> planning.
> >>>>
> >>>> We have implemented interactions between distributed charges
> >>>> (Gaussian, Slater)
> >>>> - this can be ported straightaway to the master branch.
> >>>>
> >>>> Polarization in the charge on a spring or drude or shell model has
> >>>> been in
> >>>> gromacs since 1995, but there are still issues with slow convergence
> >>>> of shell
> >>>> optimization. New solutions are appreciated - but not by just upping
> > the
> >>>> tolerance. Thole polarization for bonded terms is also implemented
but
> >>>> needs
> >>>> checking (start with the manual!). Feel free to contact me on or off
> >>>> list.
> >>>>
> >>>
> >>> Yes, I've done some simple tests with the existing algorithm.  We're
> >>> interested in incorporating some different methods, like
> >>> http://dx.doi.org/10.1063/1.1589749, which has been implemented in
> NAMD
> >>> - http://dx.doi.org/10.1021/ct600180x.
> >>
> >> Both these things should work out of the box!
> >>
> >>>
> >>> -Justin
> >>>
> >>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Dept. of Cell & Molec. Biol., Uppsala University.
> >> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> >> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> >> --
> >> gmx-developers mailing list
> >> gmx-developers at gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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> >
> 
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
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