[gmx-developers] Making personal plugin
feenstra at few.vu.nl
Thu Mar 13 09:45:40 CET 2008
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 cylindrical/polar.
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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam |
|( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You Want Something Done You Have to Do It |
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