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

Justin Lemkul jalemkul at vt.edu
Fri Sep 27 20:46:03 CEST 2013

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 - 



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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