[gmx-developers] saving modified trajectory

[Joe Jordan]

Could you post a detailed description of the problem you are trying to
solve and the attempts you have made on redmine.gromacs.org 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.

On Mon, Feb 11, 2019 at 11:34 PM titov_ai <titov_ai at pnpi.nrcki.ru> wrote:

> Hello.
>
> A bit overview about the goal:
> I've been using the gromacs template for a trajectory analysis tool.
> First i have to read the trajectory, then modify it and save it again.
> As i dont need most of the information from MD trajectory i dont have
> issues with saving it in the memory.
> But creating a pdb one is not an optimal solution i've found a function
> in gromacs libs:
> "write_trxframe_indexed" in "gromacs/fileio/trxio.h"
> and its a bit unclear how exactly should i use the function
>
> Also i encountered an issue (which might be a simple misunderstanding
> from my side):
> while reading frames with
> void <project name>::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc
> *pbc, ...) {...}
> i try to save the "fr" into defined much earlier "std::vector<
> t_trxframe > saved_traj" by
> "saved_traj.push_back(fr)" which seems to copy the link to whereever the
> "fr" is stored and i end up having trajectory sized vector with
> identical links to the last frame
> is this happening because i need to save it differently or because teh
> code does not do a deep copy and ending loosing data ?
>
> Best wishes,
> Anatoly Titov, phd sudent, PNPI.
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-- 
Joe Jordan
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