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

David van der Spoel spoel at xray.bmc.uu.se
Fri Sep 27 20:21:23 CEST 2013

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.

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.

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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