<div dir="auto"><div>Hello,<div dir="auto"><br></div><div dir="auto">This is part of what I have been working on for as an extension to the analysis framework, to allow saving of modified trajectory files.</div><div dir="auto">If you are interested I can share the current state of those tools with you in <a href="http://gerrit.gromacs.org">gerrit.gromacs.org</a>.</div><div dir="auto"><br></div><div dir="auto">Cheers</div><div dir="auto"><br></div><div dir="auto">Paul</div><br><br><div class="gmail_quote"><div dir="ltr">On Tue, 12 Feb 2019, 07:38 Joe Jordan <<a href="mailto:e.jjordan12@gmail.com">e.jjordan12@gmail.com</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Could you post a detailed description of the problem you are trying to solve and the attempts you have made on <a href="http://redmine.gromacs.org" target="_blank" rel="noreferrer">redmine.gromacs.org</a> please? Writing with write_trxframe should just work but it is difficult to know if this is really the solution you want based on what you say here.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 11, 2019 at 11:34 PM titov_ai <<a href="mailto:titov_ai@pnpi.nrcki.ru" target="_blank" rel="noreferrer">titov_ai@pnpi.nrcki.ru</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello.<br>
<br>
A bit overview about the goal:<br>
I've been using the gromacs template for a trajectory analysis tool.<br>
First i have to read the trajectory, then modify it and save it again.<br>
As i dont need most of the information from MD trajectory i dont have <br>
issues with saving it in the memory.<br>
But creating a pdb one is not an optimal solution i've found a function <br>
in gromacs libs:<br>
"write_trxframe_indexed" in "gromacs/fileio/trxio.h"<br>
and its a bit unclear how exactly should i use the function<br>
<br>
Also i encountered an issue (which might be a simple misunderstanding <br>
from my side):<br>
while reading frames with<br>
void <project name>::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc <br>
*pbc, ...) {...}<br>
i try to save the "fr" into defined much earlier "std::vector< <br>
t_trxframe > saved_traj" by<br>
"saved_traj.push_back(fr)" which seems to copy the link to whereever the <br>
"fr" is stored and i end up having trajectory sized vector with <br>
identical links to the last frame<br>
is this happening because i need to save it differently or because teh <br>
code does not do a deep copy and ending loosing data ?<br>
<br>
Best wishes,<br>
Anatoly Titov, phd sudent, PNPI.<br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-2098750242437233346gmail_signature"><div dir="ltr"><div><div dir="ltr">Joe Jordan<br><div><br></div></div></div></div></div>
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