[gmx-developers] plans for GROMACS 5.0 beta December 1
dommert at icp.uni-stuttgart.de
Sat Sep 28 11:10:42 CEST 2013
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:
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?
> -----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.
> >> 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
> >> 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
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