[gmx-users] Re: your mail

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 18 13:00:50 CET 2002

On Sun, 17 Mar 2002, Adriano V. Werhli wrote:

>My name is Adriano V. Werhli and i live in Brazil. Actually I'm working 
>on my master thesis, which will be about protein folding and genetic 
>I would like to you help me in using the gromacs in this challenge. I 
>know that normally gromacs perform the energy calculation using the 
>stepest descent, but i don't need this, i just need the energy from a 
>.pdb file without the stepest descent then i'll use it in a genetic 
>algorithm to found a minimum enegy maybe better than that from the 
>stepest descent. 
>If is possible i would like that you try to show me which part of 
>gromacs i should use to do it, or indicate someone that can help me on 

You can either write a small script to call mdrun many times and do zero 
dynamics step, this will give you the energy in the .log or ,edr file. 
But an alternative is to edit md.c or steep.c 
The most important function call is do_force, it computes forces and 
energies, but there are also quite a few function calls to prepare data 
structure for the force calculations etc.

Furthermore, I suggest you pose this kind of questions to the gmx-users 

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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