[gmx-developers] Reading unprocessed topology files

[Pedro Lacerda]

Ok, I submitted the change for review. Some questions:
-- What is the legitimate use of -conc?
-- Because -conc don't take existing ions in account the purpose of the option was defeated?
-- Is guaranteed that atoms of same residue are contiguous?
-- Search residues of size 1 with charges different than 0 is a feasible way to detect existing monoatomic ions?
-- Is issue #871 still relevant? http://redmine.gromacs.org/issues/871
-- Is fix low priority bugs for release-4-6 relevant given that 5.0 is coming?


Sorry any disturb.
Thanks,
Pedro Lacerda

---- On Wed, 29 May 2013 09:05:34 -0300 Mark Abraham <mark.j.abraham at gmail.com> wrote ---- 


Yeah, I took a quick look, and inasmuch as it seems to be removing a code path that's been known to be buggy and unfixed for 5+ years and in the process fixing the genion-writes-a-stupid-log-file Redmine, that's appropriate for release-4-6. 

Thanks,


Mark



On Tue, May 28, 2013 at 5:45 PM, Pedro Lacerda <kanvuanza+gmx at zoho.com> wrote:
 ---- On Mon, 27 May 2013 13:04:53 -0300 Roland Schulz<roland at utk.edu> wrote ---- 
 
On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote: 
 > The lack of modularity in this code is its most obvious quality. My usual 
> recommendation for these kinds of questions is to pick a GROMACS tool that 
> does something close to what you want, look at how it populates a data 
 > structure, do the same thing, and work out how to get the subset of data you 
> really want. new_status() probably (over-)fills your needs. 
 

@Pedro: What is the reason you need to read a top file, and cannot 
 generate a tpr first and then read it? 
I _guess_ that is possible to use the TrajectoryAnalysis for this task, but is semantically incorrect.
I don't know where to push the attached genion.c. May I submit for review in release-4-6?
 


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