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

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 27 21:12:36 CEST 2013

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 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

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