[gmx-developers] saving modified trajectory

[Paul Bauer]

Hello,

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.
If you are interested I can share the current state of those tools with you
in gerrit.gromacs.org.

Cheers

Paul


On Tue, 12 Feb 2019, 07:38 Joe Jordan <e.jjordan12 at gmail.com wrote:

> 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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