<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"><html><head><meta content="text/html;charset=UTF-8" http-equiv="Content-Type"></head><body ><div style='font-size:10pt;font-family:Verdana,Arial,Helvetica,sans-serif;'>Ok, I submitted the change for review. Some questions:<div><br><div>-- What is the legitimate use of -conc?</div><div>-- Because -conc don't take existing ions in account the purpose of the option was defeated?</div><div>-- Is guaranteed that atoms of same residue are contiguous?</div><div>-- Search residues of size 1 with charges different than 0 is a feasible way to detect existing monoatomic ions?</div><div>-- Is issue #871 still relevant? <a href="http://redmine.gromacs.org/issues/871" target="_blank">http://redmine.gromacs.org/issues/871</a></div><div>-- Is fix low priority bugs for release-4-6 relevant given that 5.0 is coming?</div><div><br><div id=""></div>Sorry any disturb.</div><div>Thanks,</div><div>Pedro Lacerda<br><div id="1"><br>---- On Wed, 29 May 2013 09:05:34 -0300 <b>Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></b> wrote ---- <br></div><br><blockquote style="border-left: 1px solid #0000ff; padding-left: 6px;"><div dir="ltr">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.<div> <br></div><div>Thanks,</div><div><br></div><div style="">Mark</div></div><div><br><br><div>On Tue, May 28, 2013 at 5:45 PM, Pedro Lacerda <span dir="ltr"><<a href="mailto:kanvuanza+gmx@zoho.com" target="_blank">kanvuanza+gmx@zoho.com</a>></span> wrote:<br> <blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u><div><div style="font-size:10pt;font-family:verdana,arial,helvetica,sans-serif"><div>---- On Mon, 27 May 2013 13:04:53 -0300 <b>Roland Schulz<<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></b> wrote ---- <br> </div><blockquote style="border-left:1px solid #0000ff;padding-left:6px"><div>On Mon, May 27, 2013 at 9:56 AM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote: <br> > The lack of modularity in this code is its most obvious quality. My usual <br>> recommendation for these kinds of questions is to pick a GROMACS tool that <br>> does something close to what you want, look at how it populates a data <br> > structure, do the same thing, and work out how to get the subset of data you <br>> really want. new_status() probably (over-)fills your needs. <br> <br></div><div>@Pedro: What is the reason you need to read a top file, and cannot <br> generate a tpr first and then read it? </div></blockquote><div>I _guess_ that is possible to use the TrajectoryAnalysis for this task, but is semantically incorrect.</div><div>I don't know where to push the attached genion.c. May I submit for review in release-4-6?</div> </div></div><br>--<br> gmx-developers mailing list<br> <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br> Please don't post (un)subscribe requests to the list. Use the<br> www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br></div> -- <br>gmx-developers mailing list <br><a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a> <br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a> <br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.</blockquote><br></div></div></div></body></html>