[gmx-users] Re: your mail

[Anton Feenstra]

David van der Spoel wrote:
> 
> 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
> >algorithms.
> >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
> >it.
> 
> 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
> mailing

There is another option available which would not require modifying
the code. You can combine all your .pdb files (for a single system)
into one file, which can be handled as a trajectory by Gromacs. This
file can be read directly by mdrun using the -rerun option. This will
give you the Gromacs/Gromos energies for each conformation. Of course
you will also need a matching .tpr file to describe your system's
topology and forcefield (make using pdb2gmx and grompp).


(By the way, this mail indicates the usefulness of posting to the 
mailinglist: more people read your question, so you can expect a 
better and often much quicker answer.)

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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|  \__/  | "Jesus Can't Save You, Though It's Nice to Think He Tried"|
|        | (Black Crowes)                                            |
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