[gmx-developers] Fluctuating charge code, Q-Chem interface, force matching.

Lee-Ping Wang leeping at stanford.edu
Sun Nov 4 20:43:21 CET 2012

Dear developers,

I'm a postdoctoral fellow in the Stanford Chemistry department working with Vijay Pande and Todd Martinez.  I earned my Ph.D. from the MIT Chemistry department under the supervision of Troy Van Voorhis.  I've been using MD software as a central part of my research for over five years, and I am definitely a big fan of GROMACS. :)

Over the course of my Ph.D. I did a lot of method development in Gromacs.  I'm writing to find out whether there's interest in integrating any of my contributed code into the Gromacs code base.  

My contributions are in three main categories:

1) A fluctuating charge code following the work of Steve Rick and Bruce Berne, with further improvements following the work of Jiahao Chen and Todd Martinez.
2) A QM/MM interface with Q-Chem, mainly following the existing QM/MM interface with Gaussian.
3) Energy and force matching code for force field optimization.  This consists mainly of adding analytic first and second parametric derivatives for the energy and force terms into the low-level subroutines that compute the force field contributions.

Items (1) and (3) are incorporated into an upcoming publication which was just accepted to JCTC.  

These methods have been implemented into version 4.0.7.  Most of the code (perhaps 95%) is in separate files with as little modification to the original code as possible.  All of the functionality is controlled through the input files and command line arguments.  There is no performance impact for normal MD runs because the parametric derivatives are only switched on when requested.

If there is interest on your side, I'd be happy to do all of the work.  I think the work involved is mainly (1) updating the code to be compatible with the latest development branch, (2) writing unit tests, and (3) creating documentation.

Please let me know and I'll do my best to follow the directions on the Gromacs website and stay in touch.


- Lee-Ping

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