[gmx-developers] Making personal plugin

[Anton Feenstra]

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 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.

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).


-- 
Groetjes,

Anton
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|  _   _  ___,| K. Anton Feenstra                                     |
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