[gmx-developers] Possible Cryo-em Contribution

Roland Schulz roland at utk.edu
Wed Feb 17 01:26:26 CET 2010


I'd suggest to use http://repo.or.cz/w/gromacs.git. Just click on fork

This way your modified version can be updated and you can share it using the
address and people can download directly packages instead of patches which
have to be applied.


On Tue, Feb 16, 2010 at 11:44 AM, Jochen Hub <jochen at xray.bmc.uu.se> wrote:

> 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,
> Jochen
> --
> ---------------------------------------------------
> 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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