[gmx-developers] Possible Cryo-em Contribution

Jochen Hub jochen at xray.bmc.uu.se
Tue Feb 16 17:44:56 CET 2010

Paul C. Whitford wrote:
> Gromacs Developers,
>      We have implemented a flexible fitting algorithm to model atomic
> structures to cryo-em reconstructions (described in Orzechowski and
> Tama, Biophysical Journal 95(12) pp. 5692 - 5705.  This is a
> different method than the one in NAMD) into Gromacs 4.0.5.  I was
> told that it is possible to contribute the code, if approved.   I was
> also informed that in order to contribute it, I should implement the
> code into the GIT version and ensure that all standards are followed
> (as described on the website, in addition to including all settings
> and map into the tpr file).  This will not be a problem.
> We have tested the software and we can rapidly fit systems with large
> conformational differences (~50 A rearrangements).  We have tested the
> code with the Amber and opls forcefields and with a simplified, all-atom,
> forcefield  (http://smog.ucsd.edu, the paper describing the webtool is
> currently under review).
> Please let me know if contribution of this method to the standard Gromacs
> release is of interest.   If it is, I will implement the code into a Git
> branch (provided one is created) and make sure it conforms to all other
> Gromacs standards.
> Thanks
> Paul C. Whitford
> Sanbonmatsu Team
> Theoretical Biology and Biophysics Group
> Los Alamos National Laboratory

Dear Paul,

I would also be very interested in such a Gromacs extension. I think it 
would be great to have it in the contribution on the Gromacs website.

Best wishes,


Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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