[gmx-developers] Running energy minimization using ga

[Anton Feenstra]

> "Adriano V. Werhli" wrote:
> 
> Hello!!
> 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.

If I understand you correctly, you generate a number of different
structures using your genetic algorithm, and then you want to have
energy values for these structures. This is a way you could do it:
1) use grompp one time, to generate a topology that describes your
molecule (assuming that your genetic algoritm does not change the
molecule, only the conformation)
2) put all your generated structures in a 'trajectory', this could
simply be a series of .pdb files combined into one
3) using the topology from step 1 and the 'trajectory' from step 2,
use the '-rerun' option in mdrun to calculate energies for all 
structures in your 'trajectory'.
4) read the energies, either from the energy file, or from the log
file that mdrun produces.

Hope this is something that can help you further!


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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