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

[David van der Spoel]

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