[gmx-developers] Possible Cryo-em Contribution

Paul C. Whitford whitford at lanl.gov
Thu Feb 11 11:35:26 CET 2010

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.


Paul C. Whitford
Sanbonmatsu Team
Theoretical Biology and Biophysics Group
Los Alamos National Laboratory

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