<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 27, 2013 at 3:40 AM, Pedro Lacerda <span dir="ltr"><<a href="mailto:kanvuanza+gmx@zoho.com" target="_blank">kanvuanza+gmx@zoho.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" 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">Hello all,<div><br></div><div>I met gromacs and molecular dynamics an year ago for my undergrad project. I know next to nothing about biochemistry or physics but I'm able to program in Python and trying to learn C/C++ with gromacs. Because I'm from Bahia-Brazil my native language is portuguese, and I did really bad on english courses, sometimes I can misunderstand you or explain myself in a confusing manner.</div>
<div><br></div><div>Recently I fixed two bugs in genion (really wasn't me but the reviewers :) <a href="https://gerrit.gromacs.org/#q,I08b019b05cf3d8511757c4665c24dcaa37968ceb,n,z" target="_blank">Fix -neutral option in genion</a> and <a href="https://gerrit.gromacs.org/#q,If2a82ace079555d8a684ea876daa947677d5e442,n,z" target="_blank">Fix genion -nq and -pq when using -neutral</a>, saw <a href="http://redmine.gromacs.org/issues/615" target="_blank">bug #615</a>, and felt me adventurous.</div>
<div><br></div></div></div></blockquote><div><br></div><div style>Thanks again for the initiative. Those kinds of issues are everywhere in GROMACS, but some impetus to pick the ones to fix is welcome!</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div style="font-size:10pt;font-family:Verdana,Arial,Helvetica,sans-serif"><div></div><div>## The question:</div><div>How can I read an topology file for populate my t_atoms (or gmx_mtop_t) with eg. charges and masses? read_tpx() in tpxio.h can use only preprocessed file formats like TPR. do_top() in topio.h seems a bit exagerated (in number of function parameters) to just parse an TOP or ITP file and populate some objects. If do_top() is the way to go, is grompp's new_status() approach reasonable?</div>
</div></div></blockquote><div><br></div><div style>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.</div>
<div style><br></div><div style>Mark</div></div></div></div>