[gmx-developers] Re: [gmx-users] programming gromacs

David van der Spoel spoel at xray.bmc.uu.se
Sat Jan 17 11:48:28 CET 2004

On Fri, 16 Jan 2004, m b wrote:

>dear all,
>I would like to try to implement a couple of new features/modifications
>into Gromacs. However, I found that the code is, mildly put, rather
>complex. I wonder if any kind of documentation about the source code
>itself (as opposed to the usage of gmx) is avaiable ?? 
>Particularly helpful would be info on:
>*) general structure and hirarchy of the subroutines
>*) definition and scope of the most important variables and pointers
>   (I presume that some variables are global due to performance
>   reasons, aren't they ?)
>*) definitions of the structures used in gmx.
First, it would be good to move these kind of questions to the 
gmx-developers list (to which I forward this message).

Second, as you have correctly found out, there is not much documentation 
on the code (this is why you get the source code :). Even I have problems 
with the complexity of the code, which makes it quite nasty to implement 
new stuff. One positive point is however, that there are many checks in 
the code, and there is quite strong use of structures which makes that the 
compiler can also help you in finding errors.

So maybe you can say what you intend to do, so that we can give you some 
pointers as to where to start looking.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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