[gmx-developers] Running energy minimization using ga

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 27 10:51:25 CET 2002

On Wed, 27 Mar 2002, Anton Feenstra wrote:

>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.

Actually it could work like this, since one always has a population of say
100 conformations. After energies have been computed for all of these
the genetic algorithm kicks in to do mixing etc. and the generates a new
traj (series of structures). That can be used with the same tpr file
ofcourse. The energy calculation would even be quite efficient.

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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