[gmx-developers] Making personal plugin
jkhao at ibsm.cnrs-mrs.fr
Thu Mar 13 15:33:35 CET 2008
Anton Feenstra a écrit :
> Anton Feenstra wrote:
>> Mark Abraham wrote:
>>> Jonathan Khao wrote:
>>>> Hello !
>>>> We're currently trying to develop a tool for gromacs which returns
>>>> the system's coordinates in a cylindrical coordinate. We're newbies
>>>> in the gromacs developement ... The trxio.h seemed to have the
>>>> right fuctions to do so. The problem is that it includes a lot of
>>>> dependencies and making tests and debugging would take an eternity
>>>> if we'll have to recompile the entire thing. Are there any
>>>> instructions somewhere on the web on how to make fast tests while
>>>> programming or any documentation on how to tweak gromacs ? If not ,
>>>> could you give us some hints or instructions ?
>>> You haven't explained well enough what you're trying to do... make
>>> an analysis tool or not? If the former, then your testing cycle need
>>> only rebuild the executable + objects + libraries that you're
>>> actually changing, by "make <executable>" in the src/xxx subdirectory.
>> If what you want is extract coordinates in a cylindrical (i.e.,
>> polar?) representation, I don't see that you need to modify trxio at
>> all. It should be sufficient to write a small tool that reads
>> trajectory, calculates cylindrical coordinates, and writes them out.
>> Presumably, this could be done (re-)using one of the existing
>> trajectory formats, since the dimensionality doesn't change. (But you
>> should be careful not to read them as carthesian...) You should also
>> be careful about precision issues, which are non-homogeneous in
>> What you *might* want to add to the gmxlib are two (simple) routines,
>> one that converts carthesian coordinates to cylindrical, and another
>> that does the opposite.
> Ah, by the way, in case you need it, some of the basic maths can be
> found in pdbio, where (carthesian) gromacs box (9 matrix elements, or
> three box edge vectors) is converted to crystal unitcell
> representation as used in pdb (three angles and three edge lengths).
Thank you for your responses. Effectively , I haven't been clear on what
we intend to do. My system is a Protein Detergent Complex, and our goal
is to know how atoms behave are along the faces of an alpha helix. So we
wanted to make a tool that read a Trr file, and converted the
coordinates as a function of :
- the position along the axis of the protein ( fitted to the Z
- the distance from the axis
- and an angle
So correct if I'm wrong, as you suggested, the use of gromacs's
functions to read the "trr" trajectory is not worth it, a custom made
tool should therefore be more appropriate ? If so are there any
instructions on how to "decrypt" the "trr" files ?
I've also been working on an other project for some time. I wanted to
get properties of some molecules (detergents) which are in the vicinity
of my alpha helix.
The properties that I want to get are avaliable using the gromacs tools.
But where I need help, is in the selection of the molecules in the
I've done verry heavy programming scripts which computes the distances
of each molecules ( degergents ) with the g_mindist , then i read each
of the "xvg" files , got the intervals where it was under the cutoff
value, made sub trajectories, concatenated them and then applyed the
gromacs tools. I suppose there are easy shortcuts to follow , especially
by avoiding the time spending printing and reading parts.
So could you help me by telling me how i could apply a filter on the
tools ? It would be verry usefull, and would at last help me to dive in
the gromacs source code.
Thank you again
Ph.D. Jonathan KHAO
31 Chemin Joseph Aiguier
13402 Marseille Cedex 20
jkhao at ibsm.cnrs-mrs.fr
tel : 0616738391
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