[gmx-developers] Running energy minimization using ga

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 27 09:22:20 CET 2002

On Tue, 26 Mar 2002, Adriano V. Werhli wrote:

>My name is Adriano, i live in Brazil and i'm asking for your help to do a master degree challenge.
>I'm trying, instead to use steepest descent, use genetic algorithm in energy minimization. 
>But to do this i need to calculate many times (generations) the energy, each time with different coordinates (from the genetic algorithm).
>I would like to know how can i call gromp and mdrun from my c program, and how can i send from mdrun the energy value direct to my c program.
>If someone can help me with it, i'll be very thankful.

You call other programs with either system or exec calls, cahck your C
To just read the energy I suggest you either run g_energy or open the
energy file your self using the gromacs library calls (see enxio.h)

The best option would be to replace the routine do_steep (minimize.c) by
your own (do_genetic or so), and code the genetic algorithm there, but
that requires a bit more programming

You should maybe also look into the Autodock code, they use a genetic
algorithm for docking and very succesful, but they do it in torsion space,
i.e. the variables are the torsional degrees of freedom rather than the
cartesian. Check www.scripps.edu/olsson

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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