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

[Erik Lindahl]

Unfortunately I think David is 100% right.

This doesn't have anything to do with how important we feel individual patches are, but there are likely ~1000 commits over a release cycle, so it might take a bit of reminders and bugging to get any particular patch reviewed - simply because people are also busy with 50 other features in parallel :-)

Cheers,

Erik

On Sep 28, 2013, at 12:05 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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
> 
>> /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
>>> --
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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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